Technically PPTP uses an out-of-band connection to establish a GRE tunnel with PPP inside on fixed port numbers, while OpenVPN transports encapsulated packets and does signalling over a single port. Presumably that makes OpenVPN more flexible. There are other pros/cons like security and device support, but I don't think those are very relevant to Ham stuff.

As an aside, I've been using Linux-based tunnels over a radio network (albeit it is a IPv6 only Wifi mesh, not AX.25) for a while, first IPIP6 + IPSec/Racoon and then I switched to TINC (in bridging mode) because of some bugs I picked up with Linux IPSec policies.

TINC with UDP transport seems to work quite reliably even in the face of lossy links, and the overhead is acceptable. Personally I find it easier to configure TINC than OpenVPN (however, OpenVPN is perfectly good over UDP also - except that it didn't work for me due to the lack of support for IPv6 tunnel endpoints).