I'm not deeply familiar with the exact philosophy of the FSF, but I would guess: (1) software freedom is mostly about protecting the rights of you as a user of

I'm not deeply familiar with the exact philosophy of the FSF, but I would guess: (1) software freedom is mostly about protecting the rights of you as a user of software, and if the government uses proprietary software on their own end to make decisions based on secret rules or whatever then that's basically their business; but on the other hand (2) there are strong arguments for making the decision making technology of government into free software since government is for and by the people who should have the right to understand the technology that governs them. So, in a way they do just want to be able to keep their own computers free from proprietary/secret binary blobs; on the other hand, advocating for government transparency goes hand in hand with advocating for software freedom (thus FSF and EFF are allies).