So what is the actual agreement between Stagecoach and JPT? If Stagecoach had purchased JPT I would have thought the existing registrations and operating licence would have transferred without needing to put in new emergency registrations.
You can't transfer a "personal license", have to apply for a new one. In this case Stagecoach have, I believe, used some slack in their existing license to operate service 118 from Hyde Road, and used the spare capacity from Middleton's authorisation, though I'm not 100% sure if they may have had their authorisation increased. Middleton depot has an authorisation for 60 vehicles, running a PVR of 44. Likewise Hyde Road depot has an authorisation for 210 vehicles, running a PVR of 171 with 191 vehicles.
The reason given by VOSA, as they were at the time, is you cannot buy a person as you would have in the case of a sole trader, or persons in the case of a partnership, so you're buying assets off that person/persons. If the company was still JP Travel Ltd as it used to be then the license would have transferred. It was the same when Stagecoach bought Bluebird, it was a personal license held by Michael Dunstan, so Stagecoach applied to add a new operating centre to their existing license.