I posted about this back in December, at the time, searching the forums resulted in nothing (My search-fu apparently sucks really really badly).
It appears (from what I can tell), because of “Frame Rate Matching” being turned on on the ATV.
But quite frankly, you want it turned on, at least here in Australia, the general consensus is to set the ATV to 4K SDR 50Hz (or 60Hz), turn frame rate matching on, and then when you play something in 4K HDR it’ll automatically switch.
If I switch Plex to using the old player, I get to keep frame rate matching and dynamic matching turned on, and the audio delay issue when pausing / resuming is gone.
I have 2 Homepod Minis in stereo pair.
Plex was also the only app on the ATV with this audio issue, I’ve had no such audio issues with YouTube, Disney+, Stan (Aussie streaming service), Paramount+, Apple TV+, etc…