Have you also noticed that the audio quickly mutes whenever the core changes the resolution ?
Yes, but I expect this to happen with emulation, since probably the emulator needs to re-calibrate and re-sync the audio to the video.
It only seems to happen on Raspberry Pi, i've tried Android and PC and they don't do it. The Android device I tried was a Firestick 4K which is a lot slower than a Pi 400.
it's weird how a clean install on a Pi 3 sets it as 'alsathread'
Not sure which version of RetroPie you're installing, but alsathread is not explicitly set as default anywhere in the latest version, regardless of Pi version. Could be that RetroArch chooses it as best at runtime.
I installed a clean version to my old Pi 3 from the Retropie Downloads section. The first thing I did was look at the audio section in Retroarch, it said 'alsathread'.
So to sum up, this whole thread was a pointless report and looks like we're stuck with it !