Needing to hold "alternate" and "interact" to heal sounds like a great improvement.
Regarding losing the biomass XP when falling into a hole, hmm, as I recall... To the left of the door guarded by the tall guys, past the ladder to storage, down another ladder, there's a hole to the left there. I wasn't sure if it was a hole or a floor, or if there might be something down there, so I tried walking over it and fell to my death. :) Going back there after, my "blood stain" was nowhere to be seen. I think the same thing happened with a hole near the entrance to the storage area, the one with a rope above it (just a dumb death, that time). I guess it might be possible that the thing spawned near the biomass station and I just didn't notice because I wasn't expecting it...
That's another small annoyance I noticed, actually. It's often not that clear when there's a hole in the floor. Yeah, the floor pixels turn darker where you'll fall through, but I generally wasn't sure if that was just a shadow or an actual hole. I don't know, maybe it never happens that it's a shadow effect, and I should always assume it's a hole...
About the whole Red Mother thing, aaah... so I sequence-broke inadvertently and that's what made things more difficult/confusing for me. That makes sense. If I never got the captain uniform, I would definitely have initiated the Red Mother fight eventually out of a lack of other options. But yeah, it's possible to cheese the shotgun guys guarding the captain's quarters. You can shoot them once while across the gap, and then they'll back up a bit and wait for you... but if you just wait (or move away a bit, maybe?) until they drop the aggro state, they'll start running back and forth across their platform and then you can hit 'em with a bullet again and kill one. Sometimes, one of them will jump/fall down to the platform below, too. Either way, once there's only one left and he's not aggro'd, you can cross fast enough with the wheel while his back is turned and murder him before he can shoot.
Anyway, if you intend to have the captain gear only available later, it might be good to change this part to really require having that other uniform first (maybe someone that opens a door only if they recognize your uniform?). Then again, sequence breaking can be fun, too. But this part is a little frustrating because it's really not clear that you're missing something. I think many people will try it again and again in the hope that they can find a timing to cross before the guards can shoot (I think Cryptic Hybrid's video shows this as well).
Ah, so I could talk to that creture next to where you get the regular uniform? Hah, he looked very menacing, so I didn't try getting close enough to talk, I guess! Or wait... do you mean where you get the blue outfit? I forgot if I killed someone for that or not, actually... but could be, that would make sense. Didn't need to outfit to get past the corridor with all the blues, though, they're not that hard if you keep your distance. :)
Finally, about the save, yeah I did trigger a new game+/reset at some point during the playthrough, though I did save after that. But if that's what causes the bug, then yeah, that would explain it. Pretty sure I was playing on 1.02.