Because it would be a nightmare to maintain a list of things to either ignore or keep. The automatic designation is simply a check of "entities" that belong to players and "tiles" that are paving. Support is added for some mods, as requested, to designate some tiles as not paving. That itself is only occasionally updated.
What I realize you both may have missed is the "radius" option. Which designates how large of an area around each player built structure to keep. A value of 6 would cause a 12 chunk by 12 chunk area centered on a single entity. This value can be used to keep the internal areas of a sparsely built base from being deleted while deleting wide expanses of explored but unused areas.
