I don't know if the engine will rotate those blocks (i call them external blocks) but they must be like that because the engine uses them to close the sides of a dungeon. Sometimes one external block will close the sides of two or even three internal blocks at the same time. One example will clear this up. I use small caps b's to describe external blocks and big caps B's to describe internal blocks.
I'd say you're spot-on. The blocks with extra geometry are used to close off the outsides of the dungeon. By stacking extra geometry into the same external block, it can be re-used to close off other blocks.
By the way, I've probably made things confusing talking about rotating dungeon blocks, as they don't actually get rotated. Rather, dungeon blocks are snapped into a 2d grid. For example, the massive dungeon below Castle Daggerfall is 3x4 blocks in size. Which geometry "faces" the player depends where that block is snapped into the grid. I was trying to convey the sense of front and back components without getting into how the whole dungeon itself was stored. I really do svck at explaining things.

I'm coding block and map support into DFConnect now, so it should be fairly easy to pop up a small dungeon viewer before too long.