[popcornmix]

Every once in a while, I get a tiny droupout (gap) in the audio. Is this likely from limiting the hdmi_clock AND using Adjust PLL together? In case it matters, I don't use the Adjust Display Refresh Rate setting because that causes a lot of resyncing to occur with my AVR and projector.

Try enabling adjust display refresh rate and see if that avoids the issue.
The "sync playback" setting may be trying to adjust 24Hz to 25Hz (e.g. for a 50Hz display) which needs resampling to be enabled.
Although I suspect you may be better off with "resample audio" if adjust PLL doesn't work well in your setup.