It's not unavoidable with Atmos.
How can panning be done in Atmos without the same issues that a virtual stereo center has?
Is it because of lower distance between speakers that shifts comb filter effects up in frequency?
I don't know much about Atmos but it seems physical speaker locations may vary considerably.
As most of us enjoy the virtual center in stereo playback, it's questionable if stereo comb filter effects are really an issue perceptionally. In normal rooms lots of 1st order reflections also cause comb filter effects. Overlay of all reflections may actually help to make such defects less audible.
A virtual center is usually higher than the stereo speaker's reference axis. So I'm asking myself if an actual center would have to be placed accordingly. On some occasions I found real center speakers easy to localize.
Once there is a center speaker and an upmixer to provide the center signal for stereo content, voices panned half way left/right would again be panned over two speakers. Problem shifted from lead singer to background vocals.
With a large array of speakers (e.g. a circle of 10+ speakers) panning can always involve at least 2 speakers.
If the required position falls on an actual speaker location, the speakers on both sides can be included.
This helps to reduce tonality changes and it's also applied for panning over virtual sources in binaural playback (e.g. over headphones).
Because of digital summation ahead to binaural playback, comb filter effects can be much more severe for such applications.
And a good room simulation can also help in this case to cover comb filtering issues with a rich set of multidirectional reflections.