At this point, it looks like there might be a bug with crop overscan in the SNES9X Next core. Turning it on results in letterboxing, which is the opposite of what should happen. Turning it off results in uneven pixel scaling.
Not sure what’s up with PicoDrive- it’s impossible to get even pixel scaling at resolutions higher than 640×480. This is not a huge deal because the Genesis itself doesn’t look any better at higher resolutions, and the scanline overlay works fine at that resolution. However, most of the shaders need HD resolution so they won’t work at that resolution. Also, it looks like crop overscan doesn’t do anything at all with PicoDrive.