I build a single small well protected base with just comfort, food, beverages, spare equipment, and only the structures required to keep my gear in good repair. Generally it only has small, immediate usage, storage and only a handful of portals (emergency, current work site, farm, and one to ta portal hub for everything else.

Because it is small, I can easily fit the entire thing on a small island, elevated pillars, buried beneath Elder altar, or surrounded by moat and/or earthen wall. Most of the other facilities; farm/ranch, metal manufacturing, secondary portal hub, warehouse, port, etc; either have no more than two 'base structures', or are places I don't spend much time at and wouldn't be too put off if major repairs became necessary. Those auxiliary places only have the defenses necessary to keep the locals at bay.

Many, or even most, of the auxiliary sites are former bases or outposts that have been repurposed.