Oh awesome! I didn't know about the area 9 shortcut. Well done! I'm almost certain there are better pathing options for many of these stages; this is just what I came up with myself. I routed this so long ago that I honestly don't remember the justifications behind a lot of it (i.e. there might've been other paths that were faster but less consistent, or required certain enemy despawns that I couldn't control properly). I'll try to help if I see something in a WIP that looks slow or if I remember anything, but I didn't keep great notes for this run.
I'm realizing now that I never even posted my RTA run here. I'm sorry! Even though you clearly saw it, I'll post now so others can find it more easily:
https://www.youtube.com/watch?v=zD8Nd0BcqD8
Re: the male, yes! Or rather, not through the walls, but you can actually get up to the boss door from below. I'm really proud of that clip. Not really sure why I didn't make a video of this before, but I've remedied that now (warning, audio seems extremely loud):
https://www.youtube.com/watch?v=D7LfXu5WxeM
IIRC, the vertical grapple before the damage boost forces your hitbox upwards a little. I seem to remember needing to do that to actually get hit by the soldier at the top. Everything prior to that is just manipulating him into the proper spot and making sure I can grapple high enough. This was done in real time, and with the intention of being consistent for RTA, so it is likely that there's a faster setup for a TAS.