The addresses I posted before fix more of the animated tiles, but it is still not perfect. I think those addresses are correct, but the way I described indexing the animated tiles is where I got it wrong. The interesting thing is that it worked for like half the tilesets even though it was not really right.
Anyway, I'm making major headway into how the game handles the animated tiles, but it's a slightly slower process than I'd like.

Update. I spoke too soon; that first formula I gave was pretty close, there's just a tweak below.
For the hardcore enthusiasts out there, I just realized that the 2-byte tile formation data is already in the SNES background tilemap hardware format. So the game itself only uses the unmodified tile formation data, even for animated tiles. But what it does is copy the special animated graphics right after the normal graphics, and then overwrite the animated set every 8 screen frames. So from its point of view, it's just a standard:
vhopppcc cccccccc
v=vflip, h=hflip, o=priority, p=palette, c=index (a full 10-bit tile index!)
So Pinkpuff, if you are using what I posted before, there are some small tweaks in order to interpret more correctly:
- Firstly, you need to use all 10 bits for the graphic tile index. This actually adds even more non-animated tiles after the animated ones
- The animated tiles are only for those with graphic tile index 120-12F (hex). Again, above this I think are more non-animated tiles that can be treated as normal
- And the major index is only 2 bits instead of 3 (or a mask of 0C instead of 1C).
I tested this with house, town, castle int/ext, the caves. Even the robot gears work now and other parts that I think used to be > 130. One tile that does still look wrong is the one that shows at the top wall of the Giant's CPU map (actually, is that long red rectangle supposed to be there? maybe it is right...).
I hope that helps, Pinkpuff! Sometimes it just takes a few iterations to get perfect.