Is there a good rule of thumb for when it's all right to have a discontinuous mesh, particularly if the mesh will be rigged and animated? For example, I've modeled a boot and to make handling the edge flow a bit easier, I modeled as three separate pieces and intersected the geometry. I'm now unsure if this will cause headaches when I go to animate or even texture the mesh.
uv and texture should not be too difficult in pieces but animating it to act as one shoe while in pieces will indeed take extra effort...
That looks like a good candidate for the mesh deform modifier and a mesh "cage". The idea is to make a simple mesh that fits over the boot/shoe, then bind the pieces to that cage using the mesh deform modifier. The cage is then parented and weighted to the character armature to deform with the leg, foot and toe bones. All of the separate pieces will deform uniformly because they are all being deformed with the cage.
Good luck!