I was wacthing a verified run and I've noticed that the runner saved the game during speedrun. I refer to this speedrun (at 45:19): https://www.speedrun.com/pe2/run/y6x2j5qy
Therefore sorry, but from what I know if saving (or using continue) the run becomes a segmented one and then in specific games if saving, then exiting and loading the save; this could make some change in terms of gameplay like less enemies or other.
I could understand for 100% kills runs which take more time than any% runs, but even there single-segment runs and segmented runs and should be splitted.
I watched the section you mentioned but not the entire video. Segmented runs are definitely not accepted but if someone wants to make a save for future practice and accept time loss then that is ok. Or they could have made the save Incase they messed up but wouldn't end up submitting the run in that situation.
Enemy spawns are static in this game so there would be no advantage to exiting and continuing outside of you dying.
He did save but save was not used, so it is still a single segment run, if the save was used then yeh it would of been segmented, if anything he just wasted time towards his run. It seems fine to me.