This is the silly anti-psyker bubble, isn't it. Considering I play
GK and Daemons, I shouldn't help you at all
BRB p78 says that you use the hull of the transport when measuring to a unit embarked inside it. So the Runic bubble is still in effect...and since you're in a transport, that bubble got much larger.
So yes, the Runic effect still works, just measure using the hull of the transport.