I was using the new 4.6 MVPs on Derelict (while using FSO 22.0). It worked okay up until the "Rites of Passage" mission.
In that mission you're supposed to defend the shuttle (in this mission a Hermes escape pod model) of the Capella governor. It is supposed to dock with the GVI Luxor until the station's docking bay was sabotaged. The shuttle then goes back to dock with the medical ship GTM Alexis. Then it was ordered to go to the other side of the station to avoid a pirate attack. However it never undocked with the Alexis like it was supposed to. After the pirate attack was defeated just the shuttle is supposed to go into the Luxor's bay, however it can't since it's docked with the Alexis. It tries to force itself in while attached to the Alexis, but this means the Alexis just keeps bouncing off the Luxor and nothing progresses.
I switched my mod.ini to the 4.5 MVPs and tried the mission again; things worked fine in this case, the shuttle was able to dock and undock with things properly.
In short, Derelict may need to be touched up a little to be fully compatible with the 4.6 MVPs.