I'm not sure why syncing on the move would require a different protocol. I implemented something a while back that allows multiple IP addresses to be configured on the client side (it's in the current release). This allows you to use one of them for an internal address (when you pull up at home) and one or more for other addresses (eg accessing your publilc IP while on the move).
As I'm sure you're aware, FTP is just an IP connection on a specific port number, with a command protocol running over the top. So effectively there's no difference between that and my proprietary IP protocol.
You can use the 'upload only' sync option to upload files from the client to the server.