Right now I can't explain what I'm seeing but if you look closely to this pic, you'll see a game, running in two different emulated machines (using OpenMSX) and rendering the same scene.
Both are performing quite different, the MSX2 (right pic) has slightly larger times processing each routine, denoted by a color bar. The MSX1 is faster enough to even show the yellow routine being executed inside the frame, in the MSX2 there's no yellow at all. Looking at the core routines, the colored bars in the last third of the screen you can see that they're being executed first when running in the MSX1.
The VDP has nothing to do, they're executing the same code and in fact, MSX2 accesses are faster. There's no RAM contention in MSX and AFAIK the wait cycles are the same at least between an MSX2 and a MSX1. I can only think in the H.TIMI or H.KEYI being heavier in a MSX2 machine; but this looks weird to me.
I've also tested a HB-700P with exactly the same results and even BlueMSX, with this same behaviour.