I've been running a Mac three display system for 5+ years now, maybe even longer. A 27" iMac with two 27" Thunderbolt displays on each side. It mostly works well... I haven't really seen (or been bothered by) most of the problems that OP complains about. The only thing is these thunderbolt displays are getting pretty old, and Apple isn't making any more similar displays in this category. I've already replaced the guts of both of them as parts have failed, and one of them has a persistent problem with the thunderbolt cable, to the point where I had to use a separate cable rather than the built-in one.

I admit I do get annoyed that even in a mostly unchanging environment (same monitors plugged into the same ports forever), macOS forgets where windows are supposed to go.

Another thing is the OS's handling of plug in events. When you have just one monitor on and plug in another one, the main monitor blanks briefly, then both monitors turn on and you're good to go. Not too bad. But when you have two monitors on, and you plug in a third, it first blanks the secondary monitor, that comes back on, then it blanks both the secondary and main monitor, then they both come back on, and then the new monitor turns on. Super irritating.