History had been changed with the dispersion of the Delphic Expanse (which was now just a regular region of space). Of course the events that happened worked to create the timeline we know from the later (in the timeline) shows. So while the Xindi joined the Federation (and served on the Enterprise J) the Xindi may have not joined the Federation in the primary universe.
But thats just speculation. Any number of explanations could be made.
No, I think you hit the nail on the head. The Enterprise-J that we saw in "Azati Prime" was from an alternate universe where the Expanse grew unstopped from the 22nd century to engulf most of future Federation space by the 26th. Was the Enterprise-D flying through the Expanse in every episode of TNG? No. That's because the Sphere Builders were stopped by Archer. If he hadn't stopped them, then the future we see in Azati Prime would have come to pass, and not TNG, DS9, or VOY. Obviously the Xindi eventually became Federation members in that alternate timeline, but not in the prime one.