It's just one of the game's many abstractions, and in this case it's a bit of a limitation on transports. IMO the rules here are pretty clear. I'll break it down.
A) To check LOS, the rules have us physically look from the model’s perspective.
B) Models in a transport are not on the table, so you cannot do this.
C) For the purpose of firing a shooting attack (including a psychic shooting attack) only, the transport rules grant permission to draw LOS from a fire point instead of from the physical model.
D) No permission exists for using any other rule (except IG officers giving Orders from inside a Chimera using its command vehicle rule), or for drawing LOS out of (or into) a transport in general.
E) Thus, Anrakyr can’t use MitM from inside a barge, Coteaz can’t use IBEY from inside a Chimera, etc.
For those observing that it would make logical sense for a model inside a CCB to be able to draw LOS, that’s true, but it’s equally true that it would make sense for enemies to be able to draw LOS to him. The abstraction of the transport rules is also the abstraction protecting your guy/s in that open-topped transport from being shot, which is (on the whole) generally a benefit to them which outweighs the occasional time they’d like to be able to draw LOS out of it.