Although I think the idea here is cleaver (and I can see how great it would be to put the Clocktower below a Bomb Boy Factory) in practice this is usually a wasted effect. There need to be both "when you build" rooms in the discard pile and a place to put them in your opponent's dungeon where they might show up.
It's not bad for just a fun card, but I'd rarely choose to use him instead of the other bosses we have.