Should be allowed to skip it since it's not even required in a regular playthrough. Most of the skips that Any% uses involve out-of-bounds clipping so it's those that aren't allowed in Glitchless. Things like skipping sections that aren't required or jumping across gaps that would otherwise require a puzzle? That should be fine! The rules are still being worked anyway on as far as I know.

The 2nd fight with Diego is completely skippable just like it was in the original.

Yes, the game does try to push you towards going to the escape pods, but you don't have to.