Let me preface this by saying I haven't worked with carbonite, but I have done extensive work with the map system.
The indoor minimap transparency issue is unavoidable, it can only be fully hidden or visible.
The alignment issue sounds like a miscalculation in carbonite. Even indoors the minimap lines up no-problem with the map:
This is a bad example because it doesn't look like I lined it up correctly (if they were, the other textures would be even bigger), but it's the only indoor shot with terrain tiles I have right now. They *can* be lined up, but the problem is it still looks looks like crap because the terrain tiles are completely separate from the textures they use indoors.
Outdoors there's no reason it shouldn't line up:
