It wouldn’t have to be a “wall” as big as an overmap tile. It could also be a giant turret tower, or a mortar emplacement, barbwire field, extra large minefield, or some similar structure that “denies” a large area but doesn’t physically cover every single square with a solid wall.
Speaking of which, why don’t we have Mountains? That feels like a relatively easy overmap terrain type to implement. They wouldn’t even need to have Z levels above them, just have some giant solid walls that you could avoid, or optionally tunnel or cave through. Wouldn’t even need Z levels above them to look good.
Alternatively, you could build a “Settlement Beacon” or something like that which guarantees that zombies (and @#$@#$ NPCs) can’t spawn in any adjacent map tiles. It would have the same effect: make sure @s and Zs can’t spawn inside supposedly locked bases, but could still approach those areas on foot after spawning 2 tiles away (at the edge of the reality bubble).
Lastly, how hard would it be to make a “secondary reality bubble” centered on a player base instead of the player?