Are protocols that are not IP compatible allowed for data traffic on our VPN?

Yes, but only if you create a simple, automatic tunnel for your VPN. If you select the 'Bridging' option on Safepipe, non-IP protocols, or protocol suites like AppleTalk and IPX, are allowed to pass through the tunnel. You may use this option if you wish, for example, a remote office to have complete access to all networking resources on your LAN. Bridging is not very efficient in keeping network traffic down, so you should only enable bridging if it is actually required. Also bridging should only be enabled for the relevant protocols.

You select the bridging option in Safepipe's 'Automatic Tunnels' section, and you select the relevant protocols in the 'Bridging' section.