On the other hand you can actually cut down on some facilities which have larger versions (living quarters, workshop, stores), hyperwave decoder still makes radars obsolete, base defenses are still pretty useless (unless built in impractical large numbers). Other facilities actually combine multiple functions (HQ). Manufacturing bases aren't really a thing anymore (at least for me), as you can't manufacture stuff for profit anymore due to balancing. Also the number of scientists you are able to use is drastically reduced due to limited research facilities with vastly lower research space. In vanilla one laboratory = one living quarter, here it's more like one living quarter per three research facilities.
Similarily I'd say that X-Com animals aren't needed (I find them quite useless tbh) and alien containment/prison facilities kind of flow into each other (meaning you probably need multiple prisons in the early game, and multiple containment facilities in the late game). They become redundant as you work your way through the interrogations. I also found myself needing multiple gyms per base in earlier versions, with how max stats are currently you can probably squeeze by with one.
Then again I also my recruitment office submod to streamline agent vetting and I have also upped the limits on prisons&containments for convenience.
I still find that base numbers are dictated more by UFO detection (and craft range/speed) rather than by limited space.