The Thermal Plant and a small handful of other areas has fake walls (aka things that look like walls but are passable) so there might be a much more obscure way to reach the thing you're looking for (I have a faint memory of a gun upgrade being hidden in a large room designated as something along the lines of "the reactor" through an easy-to-miss pipe leading offscreen). I also remember there's an area reached through one of the "indoors" areas that doesn't connect to the main maze, that's probably what you're seeing. (The area has a bunch of jars, but it's mostly an excuse to respawn everything in the room you just left :P)
Rattleskull Valley used to connect to That One Level (the brutally difficult, unfair and unfun bonus level) but I moved it to a more hard-to-find location at the last moment. The area just ends in the middle of nowhere now if I recall correctly.
@ Saving Voice: [spoilers] I distinctly remember an ending post-credits scene (which I never actually made) where Cain explains to Daphne that "mom's not going to come home" and it reveals that she's his daughter (and Cain/Voice was a couple in the past that split up) and she stuck with Voice after they divorced... so saving her is probably non-canonical. Not sure if there's an actual way to save her buried in all those lines of code I haven't touched in a decade, but I suppose my patch notes know best :P
(Saving her would involve going to the Water Tower after you regain control... potentially before going back to the truck to avoid wasting time, I'd guess?)