There shouldn't be any reason to maintain a separate 5.1 setup. I don't know of a single person local that does who enjoys spatial audio. My own room was 5.1 for a while, then 7.1, 7.2.2 and finally 7.2.4. No issues encountered with sound quality expanding out. 5.1 didn't change, though changing preamps did impact things due to how different manufacturers handled things. Denon/Marantz can force upmixing if not using Pure Mode on some models. I ran into it on my 7702MK2 and it was one of the reasons I got rid of it. I suspect something like that is happening if 5.1 somehow sounds worse on an Atmos setup.If you have someone close to you with a proper Atmos setup, go listen
I do have someone nearby with very much a proper Atmos system (complete with four ceiling speakers...all driven by a Marantz 8015) and it sounds amazing with Atmos media . However...as previously mentioned, he also has the means to keep a completely separate Classe/Jamo -based system in the same room strictly for 5.1...because it doesn't sound so amazing with that dedicated material.
One more thing related to resolution differences: I can easily switch between PCM and DSD (closest to 24/192) on my Oppo 205 when playing SACDs...and the clarity difference is immediately noticeable with something like Beck's Sea Change.
You verified this is the exact same mix and you've done this with assistance to allow for completely blind level matched testing right?