To answer some of your questions,
If you want 7.2.4, you will need the 3060 and you will need to add an amplifier. I think separate amps for all channels would help take some strain off of the AVR, and that would help it last longer, so, for the sake of long-term reliability, separate amplification does help future proof your system.
I think the StudioMinitor 65 are fine speakers, but they are not my first choice at that price point. For that same price I would be looking at some
Ascend CMT-340s, which can be used as a horizontal center speaker as well. For a bookshelf speaker that can be used on its side just fine, look at the Revel M16 or the
KEF Q100s or Q300s (good deal at the moment). Ascend CBM-170s would do well for side and back speakers for a CMT340 font stage, and the Q100s would do well for the surround channels for a KEF front stage speaker set.
For in-ceiling speakers for the Atmos height channels, I would be looking at some
KEF in-ceiling speakers with a 6" woofer. If you have a high ceiling, look at some
Hsu in-wall speakers. If you don't want to cut holes in your ceiling, look at some
JBL 8320s, and if those are too large for you, look at some
SVS Prime Elevation speakers. The JBLs would be a lot more powerful though.
For subwoofers, I would be looking at a pair of
Hsu VTF3 mk5s, and I would not wait to order them, they are at a very good deal at the moment. You won't do better for the money.