I actually suspect at least some of the removed time warp sequence effects are still hidden in the US/EU rom somewhere, just disabled or perhaps simply hidden out of player view. The gradient effect at least can still be spotted if you've got a good eye. At the end of the sequence, there's a moment where the mode7 plane flattens out before the scene changes. There's actually a short but clearly visible moment (just after the 3:40 mark in the GBA video from my previous post) where the entire screen abruptly flickers to a brighter shade before becoming darker again. This brightening effect is the HDMA gradient effect being switched back on briefly, so this effect is still in the rom, but normally disabled (they missed a spot in this brief moment). I also wonder if the other half of the mode7 plane (the floor) is also still present inside the rom, either disabled or simply out of view due to the different steeper camera angle. You can only see the ceiling in this sequence, so it's plausible the floor is actually still "there", just hidden from view.
This shows how incompetent the people behind the GBA port were. This scene is completely ruined and looks like garbage. Not only the "floor" is missing as you mentioned, but also the gradient effect. Even the soul representing Dahos' soul seems to look wrong. They definitely rushed this port for quick cash and did random job and didn't care about the details.
Just to clarify something. In this particular case, the blame lies on the US/EU localization team, not the people who originally developed the port. The time warp effects were properly ported over in the initial Japanese release of the GBA version. Here's what the JP GBA release looks like (it's not supposed to be this slow, imgur slowed it down when I uploaded it for some reason)-
As you can see, the only real change from the SNES original is the brighter color palette (which I'd guess could be fixed via hacking). The mode7 effect still has both the ceiling and floor planes, the transparent gradient is present (again just brighter), the flashing effect is still there, as is the original animation on Dhaos' soul.
It was the US/EU localization group that decided to ruin this sequence for some reason. I do not know why they did this. The only potential explanation I can think of is fear it might cause seizures or nausea.