I agree with what others have said here, especially the point about turning the room. That would seem to be your best overall option in this space.
I've bought AVRs from A4L before from both Denon and Marantz - no issues at all. If you can score a bargain, go for it.
Agree also with the point about 2 subs. I'm a HSU guy myself but SVS makes a great product too, by all accounts.
Finally, I think I'd buy speakers for a 5.2 setup right now and just have the in-ceiling Atmos speakers wired at this point. Buy the best speakers you can for the 5-channel and see how it sounds. You may be perfectly happy and decide you don't need Atmos. That room setup isn't going to be ideal for Atmos no matter what you do, so I think you could end up 'chasing' a problem that is really, really hard to fix in that room if you do everything right away. This way you get the 5-channel setup right and then add the in-ceilings later. If you love the sound, great, but if not, you know where the problem is.