Will anything be subtracted from the run if we miss the full skip by a frame and stop the timer without skipping the credits, but still taking the time to?

I'm not going to take a meme category too seriously however, if you didn't skip the credits in your video no time will be subtracted because it is invalid, re-timing could be done if timing down to the frame but honestly I suspect there will be tied WR's no matter what happens even down to the millisecond. The main concerns should be with the full game currently.

Also is there any plan to make IL categories for the Prolouge, Dutch’s Island, Whitetail Mountains, etc.

Hard to say whether doing single regions would be considered IL's or not since they seem to take a decent amount of time to where it could be a main category with sub categories for each region, once things are more routed out and potential skips/exploits are found a better answer can be given but there should be no issue either way

Yeah.