Livernois has a pretty decent rep in the mustang world in terms of motors/tuning. Mmr has been drug through the mud recently with some pretty damning accusations. Sure, no company is perfect. But they came in the thread and made it 100 times worse in a very public/highly viewed thread. Why not just come out and ask livernois why the extra money for the tune? It sounds like the reason you've mentioned, which is understandable.
Livernois has better customer service and their pricing is adjusted for that. MMR probably makes just as good of a product but doesn't have the customer service that Livernois has and MMR's pricing shows that. MMR does their best, but people give them a bad rap because they bought MMR thinking that it was Livernois.