I'm building a scale cut scene of vader and his escorts in the trench run and I'm making the cockpits so they can be opened and looked in so which way do I orient the windows ??!?
You make them the way you see them in the trench run, with the vertical bar splitting the window in half. Why? Because the primary point of view is going to be from outside the trench in your model, and you won't be able to see from the inside to notice the beam's in the way.
External models of tie fighters used in the movies always have the vertical bar, so if you're trying to be accurate to a fault, you need to do it that way.
If it's going to bug you and you are making it for yourself to enjoy, orient it the way you see it in the internal shot. No reason to drive yourself nuts. Note that you only see the window internally a couple of times, while you see the window oriented in the way that annoys you EVERY time you see a TIE model in the movies, so you'll be breaking the external view to make yourself stop raging.
There's no in-universe explanation (the windows don't rotate, it's not an optical illusion), it's just a discontinuity between the crew building the models for special effects shooting, and the separate crew making the sets for live action shooting.
If it makes you feel better, much of the footage shot in the cockpits makes little sense; the starfields in the back windows are often moving in the wrong directions, as is the Death Star surface (as Vader approaches the trench, you can see the surface filling the back window and moving laterally, which makes no sense).
I'd make my models look like the SFX shooting models, even if the design doesn't 100% make sense. The Empire is often style-over-substance, and they would use whichever design was cheapest and fastest and most unnerving to the enemy, even if it put a beam right smack in the middle of the windscreen.