i don't know about the game but in Ep. V, in the holo-call between Vader and Sidious,
Vader kneels, that's not exactly sitting but i think it serves the point.
although you make an interesting point, until now, every holo-call i had in the game was
a standing one and it made sense.
possibly, its a matter of respect, for example when you vid-call to someone (in real life)
you will make sure you look decent out of respect, same here, possibly standing conversation
is just the norm.