Are the heights above the mains a part of Atmos?
No, just the other proprietary formats I mentioned. I actually like Auro 3D but most won't run their setup as Atmos and DTXS are close to each other in layout options (that and the lack of Auro content) I have a couple of homes and one I have Auro setup that I can switch between the formats, not ideal but still enjoy them.
For Atmos the heights would be higher and moved further back towards the MLP. I wouldn't worry about those channels if Atmos or DTSX is your main objective.i just had extra speakers laying around that I could add to the Auro setup, primarily the VOG (voice of God speaker) speaker. DTS tracks sound better than Atmos in that system layout but enjoy Atmos in the other house.
Don't let all this distract you from your goal which is Atmos. The 4800 seems like your best choice, even the 3800. The 4800 just gives you some additional options if you ever decide to change for not much more money.