I guess it would be useful to know, how much more is there to Upper Underrail than what we see in game, and does it span both North and South? Because if it did then that would make sense, except of course it would then make no sense for anyone to assume that the Faceless blockade would in any way inhibit the Protectorate from doing anything.
It is pretty big, possibly bigger in the world shown. You can see beyond glasses as you fight some mutants in the Tchortist building, newly discovered sector(I think it was bio-hazardous material processing plant of the biocorp?). along countless vents blocked. So if someone wanted it, it would be pretty easy to knock down some walls and make a tunnel connecting to the northern part.
Since biocorp ruled entire underrail, it is plausible that upper underrail too, spanned up from north to south.(although, it doesn't matter much in this case.)
...However, along with it were courses left behind, some lunatics and tons of stuff that does bio damage(along with mutants). Only biocorp knows what else is buried behind the walls. Even those crazy Tchortists knew to wall in the part of the section connection to the old facilities. Hell, we only took few step to the north and found 2 alien artifacts, deadly one and more deadly one that is alive.
My point is that
southern part of Upper underrail, at least areas that are unoccupied seems more hostile place to live than the rest of the underrail.(other than DC of course) I presume legacy of the biocorp prevents protectorates from linking the upper underrail.