There's no secret to it. Pretty much any tuner can offer you tuning for that car. I suggest checking out some of the SVTP vendors to get a quality tune.
I was contemplting having VMP tune mine, but they told me a Ford dealer needed to flash back to stock 1st. Lund said they could overwrite the Roush tune. I don't know if VMP can overwrite the Roush tune like Lund. They have stated on multiple occasions that they couldn't.
If you're looking to just do the stock Roush tune, go to any Roush dealership and they will be certified to do the supercharger install and tune. Make sure they are a Roush certified dealership.
Good luck!
I bought the PHASE 3 (675 HP) kit from VMP for my 12' Stage 3 through my local dealership and had them install it. They are very mod friendly and have a very knowledgeable tech/mechanic that is dedicated to mustang mods. It came with the SCTx4 tuner with a tune already installed from VMP. My stock Roush tune is backed up on the device just like any other tune install. Not sure what would/could be different with the 15'-16' MY?!? Unless they just hadn't developed a tune for them yet when you spoke with them??
Did you ever do a tune? I have a dealer roush tune and also was told it needs to be brought back to stock if going to an aftermarket tune... I went to 3 diffrent dealers and nobody can put it to stock??