I wouldn’t call it a poor habit. I commonly use it as well. I didn’t have this problem in UE3, but I did have a similar issue with how material IDs would be imported when a skeletal mesh is made from multiple meshes. As I commented above moments ago, when I originally posted the issue I was assured it would be fixed in the next build.
Try this: slap an Edit Poly modifier on top of your stack and reassign the material IDs at the modifier level. That way you can preserve a correct view of the texture by toggling it on/off. And if the bug IS fixed in the new build you can just delete the modifier.