If you actually think about it, having an entire vehicle impervious to teleportation inside and out is actually a fairly bad idea, for exactly the reasons we're experiencing.

If there was the ability to teleport around inside the ship, we'd be able to get around much faster. Troops could be sent to the battlefield with all the speed of saying "Four to beam".

Conversely, of course, it would also mean that enemy units could teleport into the ship (Given the appropriate information, as per teleport).

This is why the Citadel's anti-teleportation etc. devices are only turned on when the shield is up, which assumes an enemy attack anyway and also makes the shield nigh-impenetrable.