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.