I had to rewrite my post since I fooled around with flycast some more, since its been a while.
For me at least, you can now just set Flycast to Fullspeed and leave the audio Synchronization enabled to get rid of the microstuttering I was seeing. Unfortunately, there’s still no way to get rid of the stuttering when enabling threaded and/or synchronous rendering, as now enabling the threaded rendering setting disables the framerate setting (as it should now). But the Vulkan renderer seems to help a lot with the frame pacing issues.
I recorded two videos to show how bad the stuttering is between fullspeed and threaded/synchronous rendering. I recommend watching these in a video player that supports exclusive fullscreen.
Fullspeed (little to no dropped frames in video, none in real time): https://mega.nz/#!oMQ01aoC!vP5pPUG9SYAEgQnA5CTy7Ur2PjPSVCas8Q4_lr3aN5E
Threaded/Synchronous video (lots of stuttering): https://mega.nz/#!MVYE3SpA!4O1xBYkhx988PuZ_gVMFiVQHv1n68lY-wTBgxdbzf4Q
These two videos were made with the vulkan renderer.