I don't love solutions 2 and 3 because the whole point of ffomega's tilesets is to allow a wide choice of colors. Both for the ground and the castle.
For houses, it is true that some specialized color patterns exist, with just this idea.
Maybe another option is:
4) Adjust graphics such that no 8x8 part would have any transparency conflict. Concretely, we could fill the corners with black. It looks acceptable to me:
I have an unrelated other remark about these tiles. I think the darker contour color should be opaque (or almost opaque). Giving a result more like this:
The result is much better. The yellow color seems to really belong to the tiles, instead of looking like a global yellow filter over the whole thing. (Again, this is still assuming that I am using the correct technique!)
In any case, all these semi-transparent tiles associated with a lot of possible palette choices allow a huge number of combination. This is really a brillilant idea. I am very impressed from what I have seen so far using these tilesets!