I don't know anything about this place or your car, but I will pose a couple thoughts...
*Why did it take two weeks for a dyno tune and burning a chip? It could be easily done in an hour or two unless you have some crazy combination. This is assuming an SCT type chip done on-site, not mail-order.
*Why dyno the car in 3rd gear? Traditionally 5-speeds are done in 4th gear (1:1). BTW, 4th gear will show more power IME. This is on a DynoJet -- I have never used a Mustang dyno.
*I wouldn't "add" hp or even recommend thinking that way -- what it runs is what it runs. That's like when people correct track times for sea level, etc. -- sure someone somewhere came up with a formula, but it's not what really happened.
*Did you watch the dyno tuning done? I wouldn't accuse anyone of anything funny, but some of the other things you mention make me wonder if the "gains" might actually be from running the car on the dyno in 3rd gear and then again in 4th. I have seen it done before.
Again -- just some thoughts I wanted to put out there.