Dag, was about to bug aliaspider.
Snes9x-Next in RetroArch 3DS seems to have the reverse problem to CatSFC.
Setting 1:1 PAR seems to result in 256*239 at all times, even running 224-line games.
OK, so I think more accurately, the SNES viewport size depends solely on "crop overscan", not what the core is actually pushing.
With crop overscan ON, the viewport is set to 256*224 and everything is scaled correctly (overscan cropping crops to 224 lines, so it works all around).
With crop overscan OFF, RetroArch Snes9x just sets the viewport to 256*239, which works for those games which run 239, but not for the majority of SNES titles.
If you don't mind losing 15 lines, leaving crop overscan ON will give the most convenient result in that you don't need to fix scaling at every turn.
CatSFC does not appear to respect "crop overscan" at all, 239-line games simply display the full image (at 224 lines, by default, since CatSFC is hardcoded).
These seem like deeper issues than anything that has gone wrong in the 3DS port, but I'd have to test on another platform to see if the same is true there.