I did runs on all versions, the difference in them wasn't anything major, just a few bug fixes that didn't affect the runs, or shouldn't have if you actually worked to optimize your run, and they made the boss head hitbox more accurate, something that would only affect the time by milliseconds. There hasn't been any changes that really change the speedrun.

I found that just starting up the game and giving a minute after your first to 5th bootup smooths it out. I have no clue why you would have a long load time other than the settings, every load except my first is consistent across the hundreds of runs I have done. Also set all of your settings down to the minimum. If you do want to reduce peoples times then you just need to take 3 seconds off of mine.