@mitu Thanks! I think I isolated the issue though: The refresh rate. I'm not sure why, but with the Pi and the same 32" LG monitor -- smooth at 60hz. When I adjusted the monitor to 50hz and set libretro to match the 2048 sample deviance went down dramatically in all the impacted emus. But I also tweaked a bit too much to be certain that's entirely it -- but that's what it seems to be thus far.
If my fix is a red herring I'll give your advice a whirl too. Thanks for another triage tip!