I think all your concerns are valid but they are not necessarily insurmountable. The FSF or whatever other entity could do just what you suggest and seek certification within the current legal frameworks. They could also talk to the carriers and negotiate individually which is probably going to be quite annoying and slow but it's not impossible and it's not like that's not done in the commercial space. The could build mechanisms into the hard-/firmware that takes your device off whatever regulated spectrum/provider if you modify anything that is in regulated territory (as watched over by some form of maintainer-quorum-signing-negotiation-structure). I'm sure there are many mechanisms and processes one could come up with that could keep with regulatory or other control aspects while still keeping things open.

All that patent and legal business is probably a more important/existential concern and a go/nogo-factor if you want to be a commercial player in a market-driven environment and less so for an entity like the FSF.