Great to hear a direct response! Thanks for the insight on why.
What about having you just point the ship in the right direction? Either drag a 3 point axis showing up/down, left/right, and front/back or start your design with the axes predefined. A 'rotate model' might be helpful in case you started out wrong. Alternatively, instead of hardpointing with a visible mount, give the option if you only want to see the hardpoint when you're in builder mode (checkbox for transparency) . In-game, it's invisible.
For the guns, maybe allow the transparency to just be where the shots come from. If you want the shot to come from the three guns model, add the gun hardpoint to the end of the barrel(s).
It might be nice to have an explanation for how the hardpoints work in-game. If there was an explanation or guide on how it all works, then I missed it. How does saying where thrusters are help? Where should they point? Also, it might be nice to be able to directly decide the ship's attributes (in whole or part). My ship starts out with very high turning anyway, and adding a thruster makes an already ridiculous ship cheesy.