Eh....I'm still confused...maybe even more. So, the height inputs on the back of my Denon have nothing to do with Atmos? I mean, my Denon X4000 did not have height inputs, nor was it Atmos....now I buy an Atmos receiver...and suddenly it has height inputs.
You are overthinking it...yes you use those inputs for your "atmos" speakers...but don't get caught up in the terminology for a moment...you can use those inputs(heights) for more applications...not just atmos...the concept of speakers firing up toward the ceiling is one way that is advertised as being the "atmos" way...IMO that is because a lot of people couldn't place them in or on the ceiling...which is more effective...when you merely put those speakers that fire upward on top of your speaker you are dependent on the ceiling "bounce" method...the expectation that the ceiling will deliver that bounced sound back to the listener...which is problematic...it seldom happens that you have the ideal surface for the bounced sound to reach you...and doesn't account for different room configurations....so the short explanation is that putting them as you have them probably won't yield the best results...
If you decided to put those speakers higher up on the wall or in the ceiling..you would need to adjust the audyssey parameters...