For level runs (glitched mainly), can I do them on a beated map since level mission you can redo? Also is prep allowed for them, as in setting up stuff ahead of time :) (before timer starts).

I think that would probably be a seperate category like 100% Glitched w/ Prep or something like that if it were to be added. One of my main reasons for this is that timing starts on the first frame of movement at the very very beginning of the map. The only way I could think of timing starting for this is when you start the first quest. So this might be a new category in the future but we will have to think about it for a while.

I think there is miss communication. I'm referring to level runs where for example the spyglass level: "Timing starts on first frame of Guard saying "Thank you!" Timing ends on first frame of "Bam, that should...""

This this moment of time I can't find a way to retrigger the starting cutscene so a full game run w/prep is not a thing.

In other news, it is going to be a bit before I do a run since I opened a can of worms looking into the map.

I think you should be able to do ILs from a completed save, though I don't know what prep you could do with it. Also I think Copper Ageing is slower from a completed save because the 4 furnaces outside of the cave aren't there