Subs...your space is roughly 2500 to 2800 cu ft depending on ceiling height 8 or 9'. If you stick with SVS, HSU, PSA, or Rythmik as someone else pointed out you will not be disappointed as all are high performance subs.You can buy 1 killer sub such as the SVS pb16, or the HSU VTF 15H mk2 and it will do the job, but there's a good chance that the bass will not be balanced. I.E. not everyone in the room will hear or feel the same effects of the sub as the people seated in the sweet spot.
You're better off performance wise to get two smaller subs that way you can balance out the sub effect. I have the HSU VTF3mk5 x 2 in my HT space...17x18x9' ceiling (roughly 2800 cu ft as well). They take action movies to a whole new level and from a music stand point they freed up my mains to handle mid bass and higher frequencies, sounds better....the dual pkg deal is hard to beat imo.
AVR...I like
@William Lemmerhirt thoughts of adding a power amp to the 4300 since it does the processing for 11.2. Or, you could ramp up and get the 6300, but adding a power amp to handle the front channels will take a lot of the work load off the 4300.
Atmos...I demoed a Klipsch upfiring atmos system, and a Paradigm system with in ceiling speakers...it wasn't really an apples to apples comparison as the content was different. Both were effective, but the in ceiling system offered a more realistic 3D experience...if you have the ceiling access to do the wiring, I'd go in ceiling atmos.