Actually, in PTSC's own past, they have contracted with the DoD/Navy (development contract for enhanced SONAR on subs based on the Plasma Antenna tech).
And you are correct, ATCO has contracts with the DoD.
For all such contracts, they must have gotten waivers on certain procurement regs because neither company (PTSC then, ATCO now) has the appropriate infrastructure to satisfy regualtory requirements for "normal" contracting with the DoD. The DoD has "lightened up" over the years in their contracting requirements (FASA - Federal Acquisition Streamlining Act), but they are still pretty daunting for big contracts and anything involving highly technical procurements.
FWIW,
SGE