I've been recently trying to figure out the inner workings of Hohokum to whittle my time down.

I have found that a trigger for RNG(Edit: Silly English fix) on a level entrance is determined by the most previous playthough. Whatever background color was last left in that level will carry over to the next run. This works even when starting a new game, still referencing the most previous run. A fresh download of the game (so the way a first time player would encounter it) is the same as having completed the level in a previous save.

I was wondering on if there was ever a precedent on a previous run manipulation before starting your current run. It would save time to preset to a better R&G beforehand, but seems as though anytime spent in game effecting the run should be counted towards the total runtime. If that is so, is it fair to say that the R&G needs to be set as a fresh download or a completed level on the most previous run for the run to be considered valid.

If there is any confusion on what I am asking I would gladly clear it up, it's a bit hard to put down in words.

Assuming you mean RNG: If there isn't already runs of it, normally it's up to the first runners to decide what is a fair or allowed in their game. Usually in my experience though, anything that effects the game should happen while the timer is going (for example, in a Yu-Gi-Oh game, preparing a file with a bunch of good cards in it beforehand, and then transferring them over after starting the timer, wouldn't be allowed).

There's a few ways to approach it. You could create two categories, one allowing the manipulation beforehand and one not, but honestly with a game with a small community you don't want to fracture whatever playerbase you have. So I think it's just up to you, but I'd guess starting on a fresh download would be my choice.

We had something like this happen with YHTWTG, and community decided for the option that made it easiest to run (no set-up run). Could you delete the save file so that the choice is random?

You have to reset the entirety of the game data, but I do think it is easier and the right option to keep things consistent. I appreciate the feedback!