The inquisition thing for the last time was completely legal. The old gray knight codex allowed the army to take new imperial guard units and their dedicated transports. Now maybe I'm missing the point but in the rules that I have been using for I think its like 2 years now, that was fine.
Allow me to spell it out for ya. The inquisitor lord is allowed to join a unit since he is an indepentant character, for a definition check the rule book I forget the page. In the gray knight codex you can take imperial guard units. So, Doug took an imperial guard unit loaded it in a dedicated transport they are allowed to take (the valkyrie) and had the inquisitor join them.
Seriously, sounds like day one stuff to me, but not everyone gets its to easy I guess.
As for multiple armies using each others transports? I seriously am drawing a blank on this one, I know we were not allowing players to get into other players transports and I don't think anyone feilded and army where they had transports to use this way but that may have been an offical ruling that came about from some situation I did not know about.