Minerva's right on the can't be helped, and its not just a tileset issue or anything - its just mechanically impossible to have two levels of walkable space right on top of the other. You can't both walk over a bridge, and under it, for example. Best you can do is 'fake it' with a transition on either side of the bridge arch porting you to the next, you know?
I think all the bindstones in revamped temples should be checked if they haven't already, as there seems to be some secret to the old ones, as I think almost all the new ones have been reported by now...hehe.