Personally, I am actually more wary of custom dyno tunes. I am lucky to have several of the top Mustang builders and tuners right here in my area but not so many people can say that. If you took your 5.0 Coyote engine to be tuned by someone who has no experience with this engine you have a much higher chance of destruction and mayhem than running an e-mail tune. So many shops say they have years of Mustang tuning experience and still go out and blow up a Coyote engine because they had never worked on one before.
There's a shop around me that won't even touch one. But they're more GM focused anyway.