It is true, Fort apogee's location does not seem to be logical. well, not as much anyways.
There are few benefits however.(weak case to strongest)
1. It allows protectorates a REASON to transpass core city.
Protectorates seems to be doing fine on their own... and even have strength to help railway crossing while this blockade has been going on. I would assume that they have all the supply they need from the local area, but what do i know?
However, I would presume that only supply they are getting from the north are high grade guns and armors - something I wouldn't call as life's essentials. But when the push comes to shove I assume protectorates wouldn't shy away from go guns blazing during their "transport" to take over core city.
2.as you mentioned, it is isolated nowhere.
There is literally nothing in upper underrail, other than a dozen scavengers and shady cult. Perfect place to build a fort away from lunatics, lurkers, beggers and junkyard hobos.
3. building elevator from the top gives protectorates unseen, undetectable troop movement benefits.
Which can be used for "militaristic unification" against smaller communities. Railroad crossing, junkyard, SGS.