a small automatic transfer system will have individual breakers for the loads it serves. a master ATU for the whole house cuts in ahead of the entrance panel and serves everything. the concern is if a breaker fails closed, like the infamous no-trip FPE ones, it will feed unwanted circuits.
the difference is thus, overload and tripping the genset, or backfeed which could kill a lineman and potentially feeding the whole neighborhood with the wrong transfer system.
it has to be done according to code and by somebody who knows what they're doing. if you upgrade from a portable generator to a whole-house rig, yeah, you're doing it all over. that's the only way to go for safety.
when we lose AC, and we've done it for 5 days, it's not a big deal to rig the canopy, tie a tarp to the canopy where the rain is coming from and anchor the bottom with two 5-gallon pails half-full, and string extention cords. if you're on the fence, heck, set up for that and save your cash for the possible whole-house job.
and contract out the big stuff. das ist fur Experten, ja.