Burnham's parents being cited as genius scientists and staunch believers in "technological advances brought about by time traveler assistance" makes me believe that they didn't actually build that suit for Section 31, it came from the future to begin with and they pretended to make it for some yet to be explained reason.
Yeap:
The suit comes from the future via Burnham's parents, although they probably told Section 31 it was their idea or something. Won't be surprised if the Burnham's themselves are from the future.