So the new rule for IL runs states that replays are not allowed, mainly because of the fact that at the end of the level, the game transitions to the next level faster (skipping the score % screen). Instead of removing all previous runs that were done on replays (which ended up being a lot), we decided to keep them but add a sufficient enough time penalty so new runs under this new rule aren't at a disadvantage. The runs you mentioned are valid, since they were performed before the rule change and have the time penalty mentioned earlier added to them. Previously they were removed but this is not the case anymore.
I'm pretty sure that as of now IL 100% runs haven't been properly defined. The problem is that unlike in the other categories, there is no set amount of score you need to get in a level for you to get a Murfy stamp for that particular world (meaning it's non lineair). A solution to this would be to have the 5 stars at the end of the level (+all the Teensie cages) as requirements but not all consoles show the stars at the end of every level.
To skip (the skippable) cutscenes on pc you have to simultaneously press and hold the "E" "S" and "C" keys, not the "ESC" key.
I'm not a pc runner but I've heard that the refresh rate of the monitor causes it to either run 1.0x or 1.2x speed. As for the speed in the video. At first it seems to be 1.2x speed based on the exit time of FC1, though during the rest of the video it looks more like 1.0x. Might want to ask around in our Discord.
If running the game under Wine has no clear differences then I think it should be fine.