MAC addresses are generally not passed on by routers. The router keeps them in an ARP table and that can be accessed remotely if someone wanted to see them. But they would have to get into that router or into a computer on that subnet to see any MAC addresses.
If the government is not collecting the MAC addresses of devices on its secure network or secure email system then something is serious wrong.
Next they should have the router info from her service provider. No one mentioned who was providing bandwidth when she was using her home-brewed system. Verizon FIOS routers collect information on your whole network. A tech can tell you how many computers and printers you have on your network (along with MAC Addresses without asking).
If she used a provider router, everything was open. They also have the server so they know that mac address. They know the service provider once it moved off property and should have the router tables.
I suspect though that all ISPs are now collecting and storing MAC addresses to respond to FBI and Homeland’s legal requests.