Probably the federation is still trying to access matrix.example.com instead of just example.com to get the .well-known configuration.I'm not sure how to make this work in general, you need a way for the federated instances to ask your instance for the configuration in the host you want.
Syncthing is so great, I don't have to deal with things like a FTP server, sending files to a cloud drive, connecting via USB, or similar. I just point syncthing to the folder I want to replicate and my PC has it immediately and receives new files as soon as I connect to a WiFi (because of my configuration), and then at the PC I can easily backup the files.