I am currently running 7.1.2 The 7.1 layout is pretty much as specced by Dolby and has always worked well in the past. The heights could probably do with being at least a foot or two higher than currently. It's mess about in progress
I have not yet tried, but could switch the Back Surrounds to Rear Heights and have 5.1.4 now. I will may be give it a try later on.
If 7.1/5.1 discs are good then they are still good, upmix or not. Bad mixes will still be bad, upmix or not, Oceans 11 for example has almost no rear use and is I think Dts MA. Bad films with good mixes like for instance Sucicde Squad does sound IMO much better than before using Atmos. I did watch Player One pre and post Heights and that first race scene is definitely improved.
I am not entirely sure if you don't have the additional speakers setup, whether selecting the Straight or DSU/Neural X options on the Yammy gives you the Atmos/Dts:X mix for those discs if they have them or just the core True HD/Dts MA.
My memory could be suspect, so comparing like for like, after some time, with and without the additional speakers may indicate I just notice things that were there before, just more obviously.
Jason Bourne for example sounded good when it was only setup for 7.1. Having tried it with the Atmos track and front Heights, I can't say that I noticed much difference.
I have tried muting and un-muting the Marantz which is handling the Height speakers and to be honest I can't say if I noticed. However as I mentioned earlier, seems there is more interaction in the base layer so that could account for it. If having the speakers set on the Yammy means it uses Atmos rather than True HD then you would still get some effects even if the Marantz is off. If that makes any sense.