What I heard from someone with contacts in Universal is that MK delivers the songs to the record company, with some guidelines about the track list and the order of the songs, and the final product is decided by the record company following (or not) that guidelines.
About STP, the old fans from the TR Mailing List will remember that was delayed various times because there were disagreements between MK, Ed, the record company etc etc etc about the selection of songs. The first problem was the two Emmylou songs. MK was so upset that mentioned that in many interviews and decided to do a cd wih her when possible.