Hey, is it allowed to put down a speedrun tool savestate at the beginning of the level before the timer starts? The timer doesn't turn grey and the time gets updated in the journal. I don't see any reason why it shouldn't be allowed, it doesn't affect gameplay at all and things that do the same thing like ahk reset script are allowed, but I still wanted to ask before doing a run just for it to get rejected.

Unfortunately, this is not allowed, as Speedrun Tool is explicitly listed as a mod whose features are (mostly) not allowed to be used during any run. While it's true that this largely achieves the same effect as loading a level using the debug console, ultimately it still uses a feature of an external mod, and savestates are also known to sometimes have weird behavior with custom entities.

If you wanted to achieve a similar effect, you could use the "Skip Restart Chapter Screen Wipe" option in Speedrun Tool, which is one of the few features of that mod that are allowed for IL runs only, or you could still use the debug console to quickly load levels as normal.