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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.

They (the govt) can collect MAC addresses or they can request ISPs to do it. But they cannot see MAC addresses outside the subnet so the information only has use for correlating the MACs with other collected info on that subnet. Did some tcpdump just now although I haven't used it for years. Used -e which should grab all MAC address. I see:

23:00:05.197220 ARP, Ethernet (len 6), IPv4 (len 4), Request who-has 192.168.0.19 tell 192.168.0.1, length 46
23:00:05.197236 ARP, Ethernet (len 6), IPv4 (len 4), Reply 192.168.0.19 is-at 34:36:3b:c8:67:88, length 28

That's it, a grand total of one mac address in an ARP reply. I tested a capture while I sent myself an email from my own email server. Granted the email came via IMAP from Apple's server, but Apple's server is not going to get the MAC of my server either. They are not sent beyond the router. Collecting them internally from every subnet on earth has the benefit of tying it to a specific network card as you mentioned. But that is quite a bit of data collection for not a lot of benefit. Collecting them from Hillary Clinton's subnet is a bit more interesting but seems unlikely.