The problem with that theory is that he had another year and a half between escaping the end of the Universe and meeting the Doctor again. During which time, he repeatedly used the Doctor's TARDIS to travel to the end of the universe (and some distance from the original planet, depending on how close the rocket got to Utopia before things went pear-shaped). So, as long as the Master's TARDIS was closer to the original planet than Utopia (or the wreak of the rocket), he would've been able to travel to it. Considering that he's almost as clever as the Doctor, he probably would've even been able to rig up some way to tow or remote control one from the other, and keep both.