J3RK
144
Yes, I suppose you could carefully keep track of all your bands at all stages just right, but that would be a total pain too!
I guess you just kind of have to decide where you want to direct your effort. Early in the process, or trying to “fix it in post” 
My tracks are generally simple enough, and from few enough sources that I can do most of my work in the sound design phase, then just touch things up a little bit later.
To your point about too many multiband layers, I think having several, set to slightly different bands produces almost a quantization effect at all the overlaps.