The solution would be something that removes Dolby Dialnorm data, but sadly I don't think anything exists. I've tried a couple of utilities:
eac3to (an A/V remuxing tool) will remove DialNorm for conversion to FLAC, but you can't go atmos to atmos, and
MKVToolNix (a utility for working with MKV files) seems to remove the DialNorm, at least as far as the
Mediainfo utility is concerned but when you play the files back on an AVR or open them in the Dolby Reference Player the DialNorm info is still there, so there must be more metadata attached to the actual Atmos metadata that MKVToolNix can't see. I did find someone asking the author of MKVToolNix about removing DialNorm for Atmos on the utility's
github, but the software's author closed the ticket with the remark "Closing as it's highly unlikely I'll ever feel motivated enough to work on this."
I dunno if anyone has the programming nous (or inclination) to do do it, but a utility that would recursively comb through folder structures and reset DialNorm on .mkv, .mka, .mp4 and .m4a to -31dB (or remove the metadata entirely) would be very useful to people who have file-based Atmos playback capability, especially as this content continues to proliferate in the years ahead.