Maybe it really is just decimation. That wouldn't have a huge effect; decimation is painful but not catastrophic.
But most importantly, it's a game; it's not realism, it's not a training simulator. It doesn't have to be probable. It's more probable that a well-equipped, well-trained small team with the advantage of surprise and placement can destroy a platoon of moderately-equipped, moderately-trained soldiers caught unawares - that's sort of the whole concept of special ops teams, in fact - than it is that people can start doing magic with their mutated genes. Or, for that matter, that a person could take a piece of metal and a wooden(?) stick and without any tools or heavy machinery turn that into a masterfully-crafted shock hammer. Or that a little bottle could contain a controlled fusion reaction to be used as a battery. Or that cryogas would even ever be possible without completely violating one of the most fundamental laws of thermodynamics. Or that you could survive getting shot 20 times by a 9mm just because it was a little wobbly and maybe had some rust on it.
If Fort Apogee breaks your "immersion" and these things don't, then you're just using a buzzword with no reason behind it. We know the game world is abstracted - there's more to Core City than just what the player can see - the maps only exist to show interesting parts of the city. We know there's more to the caves of UnderRail than just what the player can see. Why wouldn't there be more to the Protectorate than just Fort Apogee? Or, depending on how you like to think about it, more to Fort Apogee than just what the player can see? No reason at all that there wouldn't be.
