Ok after checking this is the y correction for sprites and scroll2 which makes this bug to appear. By removing both, it's gone.
The obvious difference with both removed is that the purple defense bar is touching the top of the screen, but if it's the only drawback then it's worth keeping things like that.
edit : and apparently there is no way to have both fixes at the same time, if you fix the tree in this ryu against ken in the attract mode then sodom's stage get big black gaps. You need to move scroll2 to fix them, and then the sprites too, and so the gap in the tree appears.
So it's probably a bug of sfz3mix itself, I'll keep the fix as they are for now.