I did remember the whole clone TARDIS issue — indeed, I was fairly certain this point would be brought up. As has been pointed out, that was a deleted scene, so I don't think it counts, especially since Russell T. Davies later commented that he was glad it didn't make it in; I'd say it's not intended to "count" at this point, so the clone Doctor doesn't have a TARDIS. But I threw in the line about this TARDIS not being definitive proof as a sort of catch-all acknowledgment.
But really, I just don't see why Steven Moffat would ever use the clone when it's already clearly established that multiple Doctors can meet. It'd essentially be using a knock-off character when the real thing is freely available.
Admittedly, my opinion is somewhat colored by the fact that I really, really dislike "Journey's End." But that's a whole other matter.