When setting up Matrix, from the drop down menu of available domains I believe it offered the onion address to the FreedomBox. Does Matrix work over Tor?
Federation is not likely to work because other servers will have to understand .onion domains by using Tor. But I don’t see why a group of users on a single server can’t be using matrix-synapse over Tor. This has not been tested, AFAIK. If you test, and it works, let’s update the manual. If it does not work, then we can filter our .onion addresses from the domain list.