Sorry if I'm barging in, but only had time to read the original post and some of the recent comments
I've seen the "microstutter" in AVGNA and Freedom Planet when running under the normal Fusion runtime on Windows.
Both these games have vsync enabled, and this also seems to be the core of the issue.
I'm pretty sure this is related to
1) Fusion deciding to frameskip because the blocking vsync call is causing the runtime to think there isn't enough time to render the next frame
2) Fusion deciding to idle sleep after/before vsync, causing the next frame to miss the vsync deadline
3) the fact that these games use UFS.
It's pretty difficult to debug, so I can understand why Yves & friends would have trouble diagnosing it.
I use a different heuristic when vsync is enabled.
Initially, we don't sleep between frames at all. However, if the target framerate undershoots/overshoots, we disable vsync and use an FPS limiter.
Also, when going fullscreen, we update the device to display at the target framerate (usually 60Hz), but we still use the heuristic in case the user has odd graphics settings.
Whoever is maintaining the Windows runtime could experiment with a heuristic like this, since it's worked well for us!
Obviously, the device can't be set to use 60Hz with UFS, since it uses a borderless fullscreen mode, but maybe some savvy extension developer can extend UFS with this option