First off, that the military likely has tinkers is a thing in this story:
military-grade tinker-tech
There is no reason for that turn of phrase, or for the surrounding paragraphs where they worry about the militarization of the PRT, if the military does not have parahuman technology and resources in excess of a single branch of law enforcement.
You give statements about the "PRT Mandate" but in fact we known little about the PRT's mandate beyond statements like:
Introduction
Parahumans are contacted or contact the PRT to request membership in one of the teams under the PRT's umbrella. Smaller offices with only five or so employees may maintain only one or two parahumans working alongside the PRT office, while other teams support the Protectorate team as an independent agency separate from the PRT in all things excepting oversight, collaboration and general management.
It is a primary goal of the PRT to recruit and include as many parahumans as possible. This ensures a safe environment for parahumans; it allows for stabilized, healthy interactions between parahumans and the unpowered; and it grants the PRT the ability to better answer threats.
Which does
not state that the PRT has jurisdiction over all government-affiliated parahumans. Neither does the description in the cast page.
Furthermore, "The Protectorate" originally referred to the team of Legend, Alexandria, Eidolon and Hero, and expanded to refer to other teams
individually as the PRT expanded. That usage is specific the teams that parahuman volunteers were placed in; parahumans who volunteered to PRT authority in exchange for government support. Furthermore, we know from the same citation as quoted above that parahumans do not have to be in Protectorate teams to work with the PRT.
You attempt to cite Alexandria's oath, but that oath
does not resemble the modern Protectorate, and furthermore at the time the PRT and the four members of the original Protectorate team were, guess what,
linked with the army. So the military very specifically had, at the time, parahuman members and resources.
In short, there is ample reason to believe that
it's possible the military has parahuman resources, because they
have had those resources in the past, and
no evidence that the PRT has jurisdiction over all government capes. Which is enough to support my statements, both that the military could have capes, and that it is not supported anywhere that the PRT / Protectorate mandate includes a monopoly over government parahumans.