Wish I could help on the Apple issues but I don't use one. Can say I do get Atmos when using Netflix, it does show up on my front display. I don't use the virtual speaker settings I have those set off also. I really like, in the (Parametric EQ) settings, the YPAO: Low Frequency, mine is set to that one. Best I've heard on my set-up anyways. You gotta run the calibration, than you can choose which settings is best for your set-up. YPAO adjust the low end down to 15 Hz. Not that my speakers can go that low they can't. From what I have read, it adjust just the low end and Subs and or Subs if you have more than one Sub and leaves the mid bass and highs alone.
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As you can see my right front is a little higher on the low end, my Sub is on the left side next to the left main, guess it adjust for being close to that speaker. That something I've never been able to set that close with the low end on any Yamaha. It kinda reminds me of the way X32 was able to dial in my two Subs on my Onkyo NR818 which I liked a lot.