bsnes does weird stuff with scaling because of the HD Mode 7 and needing to be able to change resolution mid-scanline. It’s usually running at 480p all the time instead of 240p, which may explain why the integer scaling has so much leftover.
As for compatibility, there is a scant handful of terrible games that will run on bsnes but not snes9x, including A.S.P. Air Strike Patrol (which will technically run on snes9x, you just won’t be able to see the plane’s shadow; this also affects bsnes unless you choose the “accurate” dot-based PPU option), Hayazashi Nidan: Morita Shougi, which won’t run at all (it runs in bsnes but IIRC the AI that utilizes the special chip is still pretty dumb), and a couple of other obscure, never-released-outside-of-japan oddballs. That is to say: you’ll be fine with snes9x unless you’re specifically trying to run super-weird stuff.