I'm not a programmer, but I'd guess that the choppiness was a trade-off for having overlapping parallax that doesn't use sprites for one of the layers. With the layers as big as they are in Ys III and Ninja Gaiden, they would probably run into problems with sprites.
As far as I can tell, every PCE game that has overlapping parallax layers and runs at 60fps is basically using sprites for the overlapping stuff.
Are there any examples to the contrary? Better question: which emulators let you turn off the sprite and BG layers?