H&S and Bully Dog's down fall was due to there own success which put them on the EPA's radar. Although Bully Dog is more of a canned tune and H&S was a semi caned tune that was known to pop head gaskets due to the limited parameters they had access to which caused timing spikes.
They were not going to last long anyways once EFI live and EZLYNK finally became available for more brands besides GM. These tuning platforms were leaps and bounds ahead in the amount of parameters and tables that can be adjusted which allowed tuners to increase power to levels that would break stuff with an H&S. Most of the EFI or EZLYNK tuners are small compared to companies like H&S or Bully dog, and it would take the EPA a lot longer to go after all of them.
Gales recent tunes have always been on the very mild side since he does not alter any emissions equipment on modern diesels. He is too big of a company and I am sure the EPA would jump on him like a chicken on a June bug the second he did. He cannot afford to alter anything.
Tunes like those from Calibrated Power Solutions say they are "emissions intact", but that does not mean they don't alter emission controls to achieve their power numbers. For one, they turn off the EGR and put reducing NOx solely on the SCR.