It's true that a pure layer 2 vpn setup would instantly enables the bonjour service without any other configurations. The difficulty is to find a layer 2 vpn, to install it and configure it. There are probably some proprietary solutions that enable this feature. To my knowledge there is only 1 good layer 2 vpn. It's open source and it's call openvpn. It does layer 3 vpn via the tun adapter and also layer 2 via the tap adapter.
To give more details on the installation of a layer 2 vpn, one need to understand some fundamentals basic of linux and networking. The vpn client will need to be in the same subnet or also know as vlan or even broadcast domain as the other bonjour devices like printer, mac osx server, etc. In order to do so, a linux/unix server serving as the vpn will bridge one of it's network card which is in the same vlan/subnet.
For the more experimented here is a very useful document on the setup.
If it's too technical, this article seems to also be helpful for a more straightforward way of deploying a layer 2 vpn for bonjour.