The FCC does not care if you use encryption, they just want you to pay for the spectrum. As you observed, radios that can do this are commonly available, you just can't use them on ham bands. IMHO, that's not unreasonable: if you can program a radio, you can figure out how to reserve the spectrum with the FCC too.

Encryption not allowed on ham bands because it makes enforcing non-commercial use impossible. It's as simple as that, no conspiracy theory about "suppressing revolution" is necessary to explain it.