I have experience with both Sonos and structured media/whole house audio install. I would recommend you go for a connect amp as you are thinking for a single location and then play 3 or play 5s for the other areas. The control app is great and basically gives you the poor mans version of a whole house audio system without the install cost or multiple in wall zone controls. Multiple phones can be connected to the sytem at the same time without breaking it, and Iphone, Android and PC are supported. Get a NAS storage device and you are done.
If you do decide to go for a full blown whole house audio system I would not recommend installing in wall M3s as ceiling speakers. In ceiling speakers have a coaxial design that makes them less fussy about placement and also gives them a more even frequency dispersion. As you mentioned they are not intended for "sweet spot" listening and are meant to give a room filling sound without a "soundstage." In-ceiling speakers made by the likes of Leviton, pyle, niles audio, Yamaha, polk, etc have a standardized opening and can be interchanged if necessary. A 6.5 or 8 inch driver design is typically available. If you are worried about room filling sound don't bother. Even a 6.5 inch pair at moderate volumes will fill the space with even and pleasant sound if placed properly.
Typically, audiophile type concerns aren't addressed by an in ceiling situation. You know too much about good sound obviously and it is making you overthink this.
Of the 2 scenarios, Sonos or installed permanently, and given your process so far, Sonos is more for you IMO. You are obviously a tinkerer, as am I , and will forever be asking if you could have done better. Sonos is completely flexible. Placement, how many, how big, when, are all at your control. Then if you move, pack it up and take it with you. FWIW, a single play 5 will fill a 14W x 25L room with a 12ft vaulted ceiling with loud and full bodied, pleasing sound. It also wont scream "I'm a point source speaker located right here, look at me!!"
They don't distort, even when abused, and have full eq control for room boundary compensation. Can you tell I am a fan yet? So is the end user of this install.
Don't get me wrong whole house zone audio kicks ass. But it's a set it and forget it kind of thing. Do it right, once. Good luck!