Because they're not always doing secretive stuff, and even their secretive missions may start and end in airspace they have to share with friendly airliners.

Sometimes it's a deliberate "we see you", too. https://twitter.com/Gerjon_/status/1475444704250630148

That was a training flight, it's in the PDF.

I imagine operational flights might "officially" start and end as routine training flights, at least on paper.

All operations in Class A airspace, which goes from 18,000 feet to 60,0000, is conducted under instrument flight rules, which means flight plan and clearance, transponder, two-way radio, and (now) ADS-B. read this account of a SR-71 Blackbird http://b.johnwurth.com/aspen-20/