There might still be hope because I've seen many other new system announcements that mention the same line "secure, end-to-end encryption" but most of the time that refers to the infrastructure in general like microwave links, data lines/T1, internet access where used, etc.
And yes, they can have a mix of Clear and Encrypted comms. Many times they even do it on a radio by radio basis or by channel or a combination of both. I suspect that will be the case since even the article mentions they'll still be "interoperable" with Fire in their UHF frequencies.....