Player versus Friendly is a more specific implementation. The frigate copy ability is a good example. If it's running around copying other peoples frigates, you have a potentially exploitative ability, and you have a small set of viable targets(they wont get your weapon research improvements) to add to your problem. Another one is the planetary shield generator, an ally could take your planet, keep the generator, and have a shielded planet without having researched it.
As a support buff on a capital ship, it makes little sense to marginalize it's effectiveness in an allied fleet. By design, it is anyway, but if you have two Dominion fleets, it will take effect on both it's own and the allied Jem'Hadar.
It would reduce it's footprint however, and if I can't get it running better(pretty sure I can) I might do that anyway, but it's not an intended behavior.
Edit:I just added two more files into the ability so that it can leave files in residence and terminate the buffs in a more logical fashion. It's behavior will be identical, but file creation every five seconds has been reduced to only those ships newly entering range. Unaffected ships will also keep a file in residence to avoid repetitive checking as well.