Ya, you're right that a TBR could side step the fillrate hit in MSAA, it has all the information ( in theory) but it would be a neat trick and not MSAA strictly speaking. Also, there would have to at least be support for multiple z values built in so there is an added cost.
I still think this polygon limit thing is meaningless in the real world. It's a rrace between render speed and the abililty to store and sort the scene. Right now and for the foreseeable future, I would argue that if a scene is renderable in realtime, it's processable using a TBR system.