As far as I know it did the discussions about layer for tunnel and bridge not end up with an agreement to tag them without layer.
You can argue that it is not needed for simple cases but then you end up with more rules and special cases. I'd say the layer tag does not harm.
Yes, I have seen bridges in tunnels.
Updating/Extending the wiki is always welcome and the validator pages need definitly some extentions. Would be nice if we would have all messages explained with an description how to fix it.