Hmmm... I find it odd that it doesn't assign the bedrooms then... maybe the problem was the rooms weren't rectangular... in which case it needs to create less "wiggly" hallway rooms and more rectangular rooms (which would seem to make more sense anyway as human houses (at least) tend to be dominated by rectangular rooms... even hallways often are! :)

Edit: Just want to add that I agree with your strategy, I can't think of a better way to organise it without changing the result entirely and creating a cave / underground habitat / hobbithole generator where I would expect round rooms and twisty passages and so I'd probably decide the rooms, place them in proximity and then add linking passageways... so kinda the reverse of this house generator! :D