Nah, the domes are connected with tunnels, unless they lost their legs they were perfectly able to move. I've since replicated the same again multiple times later when things started really going to hell. I destroyed their workplace, homes and pretty much everything in the dome. Quarantined it, turned it off, and the ones that hadn't yet died still wouldn't move (didn't try what would happen if I destroyed the dome they were in, something to keep in mind for the future). Since I cleared everything I ended up moving them manually since I could easily select them this time around (though can't move renegades, so he just chocked to death like the dumbass he was)
As for the priority thing, seems the only way to fix the AI is using mods as the "default" AI is dumb as bricks when it comes to job preferences. Eg. if you don't specify "specialists only" (or the inverse) on buildings you'll have Geologists doing the dishes in the bar and untrained mooks mining, from the same dome. Otoh, if you do specify specialists only you often get understaffed buildings. Setting preferences on domes similarly has the risk of you ending up with *only* that specialisation in that dome resulting in trouble with utility building staffing.
Per my understanding the only fix is either dealing with it, and just letting them do whatever, micromanaging the hell of out of things, or mods (which is what I'll try next). There really should be more fine grained control of target populations here, imho.
When it comes to resource management, I kept things at default priority unless I needed them sorted asap. Though in general it doesn't really seem to matter much, and gets much, much, worse when Shuttles get involved. Eg. if you have an Electronics Store at low or medium it will still gobble up all your electronics if you're low, even if you set repairing the Drone Hub to max priority (and yes, there were active drones in range to actually do the repair), only solution is to actively turn it off.
Not sure how you'd get away with only a single colony on a map with massive elevation differences though. Guess you could flatten the entire thing, in theory, but doubt that's practically workable. The only other thing I can think of is to make each colony entirely self-sufficient, but that sort of defeats the purpose...
I'll look for some of the mods that are claimed to be essential to fix some of the AI issues and give it another go, see if that makes things more workable.