Oops, you got me there, Bish!
Truth be told, I've never really put an IC inside a transport, since we Blood Angels favor jump packs. I always thought you could, but since I've never needed to look it up, I didn't know where to find it. Unable to find backup for my opinion, I assumed I was misremembering.
So yeah, you can deploy pre-joined and already inside the transport (I always thought you could, I just couldn't find where it said when I looked for it)
Question then becomes, how would that work as far as taking turns goes? Would you deploy the IC, along with the squad and transport all as one HQ deployment, or would you put your transport/transported squad down first and when the time comes to deploy your IC you just say "You go, he's not starting on the table." (I would think the latter)
I've never been so glad to be proven wrong though. I just started a transport-heavy list <chuckles>
That said, I would still leave mephy outside of the transport, just to keep from putting half my list into one basket.