Can passive crew abilities from crew on the Phantom be used while it is docked? Like for example Jan Ors

The Phantom basically doesn't exist until it is un-docked, so no.

So far the only upgrade that has any effect on the game while the ship it's equipped to is docked is the Phantom title itself, and that's only because it specifically says it does.

Since when has the Phantom been able to dock? Here I remember that crew slot have a somewhat questionable nature due to how easily an uncloaked Phantom would go down.

Don't you just love it when multiple ships have the same name and someone titles a thread such that it could apply to either one?

PS. When Docked the attack shuttle is NOT "in play" and thus nothing that on it matters.

Cheers