Today I noticed a very interesting thing. When you use the exit save trick to overwrite AI opponents to end up in the permanent ??? money state, all of your citizens will stop to use resources like food, spices and tobacco. This even includes new houses you build afterwards. So as long as each island has 1 ton of every required resource for upgrades and food, you can easily build an empire of aristocrats for no more than stones, wood and tools.

Edit: One limitation seems to be that they also won't notice new goods. So if you used the glitch prior to having spices, they won't take note of this, even after supplying them. So it would be best to build a settlement that is as small as possible, get 1t of every good and then expand over the entire island quickly. Should speed up getting a cathedral for example.

We talked about it in DMs already. It seems like for player kills or island takeovers, the game checks the mission instantly. But for anything else, the game checks every X seconds in the background. So if you're unlucky, you might get an especially long delay until the audio message plays. As far as speeding up the following fadeout goes, it seems like finishing the mission on the lowest game speed and then switching to the fastest right when the audio message starts playing works the best. I assume the audio-to-fadeout delay is fixed but determined by the game speed you were on when it was triggered, so speeding up makes it play out faster. You can also close the game once the audio message plays manually through the save menu. The mission complete bonus is shown even before the mission complete would appear automatically. It's set as soon as the audio starts playing. That should still count as a legit end screen as long as the mission bonus is on there.

Hm, I'll try looking into that. If the time between getting the mission complete sound cue and the end screen is random, it would be a bad decision to time runes with it. The ??? money or sound cue + ? at the bottom bar might be better.

Do you know how you triggered the fast mission complete screen with this mission? I have done that mission a few dozen times and for me, it pops up way later, even if I play on the same language settings and use speedup.

It looks like there is actually more to be found. Some of these seem irrelevant but some could be useful. I found these after posting the previous comment:

1. Wireless Trading: It is possible to trade with an island with a ship or market carrier from far away by opening the trading window and moving the carrier or ship away one tile at a time. For ships, it seems to be limited to a straight line, so you cannot choose a path where the ship sprite would need to turn. This seems pretty useless but who knows?
2. Watchtower Glitch: If you place a wooden or regular watchtower inside an area you control but your warehouse gets destroyed, the area is kept in your control for as long as the watchtower is not destroyed. This is not temporary as the saved area is even kept on reloading the save. Maybe this is intended, but it’s hard to tell. This quirk can be used to keep an extension you build using the other glitch I posted above.
3. Moving Repair: If you place a ship next to a shipyard, activate its trading route and quickly press the repair button, it will be repaired while moving to its specified location. You can pre-set a trade route to just go to an enemy island trading nothing in order to attack the island while taking care of the repair on the go. This works for as long as you don’t manually command the ship to move somewhere else by selecting it and clicking on the water.
4. Breaking Building Restrictions: Click on the building you usually can only build a limited amount of. Then click on a different building group and back on the group that contains the building you originally clicked on. Hover over your land until the yellow highlight appears and quickly click on it and keep the button pressed down. Wait a few seconds and the building will eventually update. You can then build the building you originally selected as many times as you want by moving the mouse. Doing this ignores any building restriction other than the lack of required materials.

I'm not sure if there are any more glitches to be found. But if I come across something, I'll add them to the list for sure.

By the way, there are also a few small things I did not include in the video:

1. Speeding up the Resource Check: One thing I can still remember very well is that mashing the eye button for checking an island speeds up the speed at which the check is finished. Each additional click seems to half the time required to complete the check. That one definitely feels unintended and should be labeled a glitch.
2. Hiding Soldiers: You can hide soldiers inside blocks by telling them to enter a block and placing something solid there right when they enter it. This prevents enemies from attacking them unless they destroy the building you hid them inside.
3. Avoiding Curses: It is also possible to avoid being cursed by killing the main tribe house and saving after the building is destroyed but before the curse message appears and then loading the save. The timing for this is very tight though. This is similar to the fire / plague trick. I'm not even sure if curses are saved with the game though, so maybe doing this is just plain worse than just saving and loading after getting cursed.
4. Extending the Island Building Range: Placing buildings on the edge of your islands building range and removing them extends the building range by the footprint of the used building. If a house uses 4 blocks and just 2 of them are inside your range, you gain the 2 extra blocks the house used on deleting the house. This is only temporary though. The range is recalculated on saving and reloading the save. Still, it can allow placement of stuff further away by sacrificing a few cheap pioneer houses. City Gates are also useful for this since they can claim 2 extra blocks and only use stones as a material resource.
5. Building on Rivers: If you destroy a bridge or watermill, the tiles they were on can be build on, even the ones that used to be water tiles. This can be accomplished by attacking with a soldier or ship or (just for the watermill) by removing your warehouse. You can also do it by just saving and reloading if you used the prior trick to extend your building area temporary.
6. Removing Enemy Soldiers: This one only works in the original release. If you select an enemy soldier with the information tab, you can pay to release them from duty. This cost will be subtracted from the original owner of the soldier, not by you. You can delete an entire enemy army and they’ll pay for it. You can also tell moving enemy soldiers to stop this way. That one serves not much of a purpose, but it works in all versions.

I'm not quite sure I agree with labeling the save-load thing as a glitch for clearing fires and plagues. The game is old and keeping the save data as small as possible is definitely intended. They could have made it so these events would be saved with the game but they clearly decided against it. You're exploiting the way the game works. It's not a programming oversight, so calling it a glitch seems wrong to me.

By the way, I'm surprised the rules do not appear to ban the in-game cheats though. I think that should be specified, even if it's kind of obvious those would be banned for every category.

Thank you for the proper retiming. I'm not really a speedrunner so my methods are very basic. I found your runs on YouTube and imagine my surprise when I found out the research I did back then was actually picked up by some actual speedrunners ;)

To document the latest finding regarding this here as well: I did find a way to replicate this in both games and found some major uses for the resulting menu glitch. It put all into a video guide:  

Did you find any way to consistently replicate this? I tried for several hours but sadly I just cannot seem to get the backwards walk you got that may have triggered the glitch. Do you still have the save file from back then to share?

To be honest, I'd really prefer to go with option 2, simply for the sake of making the current runs more fun, reducing RNG and skipping annoying waiting times.

Any%: Anything goes, all aspects of this glitch included.

Any% - No major Glitches: While a complete ban would be the easiest way here, from what I've been told, wrong warps would make this category a lot better by essentially skipping waiting times and RNG, while not really breaking anything. Glitch Shops, setting triggers and glitch recruitments should be banned though as these are very major glitches and would make the run worse. I'd suggest any aspects of this glitch to banned that allow you to do or acquire something not possible in regular gameplay. So no glitch triggers and glitch recruits since these require glitch items that you cannot acquire in regular gameplay. Wrong warping to locations that do exit and where you can really go to could be allowed with that definition.

100pp: As the main objective is recruiting Digimon, recruits by glitch item should be banned. Wrong warps, setting triggers and buying item via glitch shop should be fine though, since they don't break your main objective that is the recruits. You'd simply have to get each recruit jingle naturally.