I don't get why we need that adjustment window at all - this sticks out like a sore thumb.
Everything else in game is configured by the way you build and interconnect it - you want an effect, add an effects computer. You want your missiles to shoot out the top? Orient the missile computer accordingly. To me that feels integrated and intuitive.
Why should thrust be handled differently? You want vertical or lateral thrust, place a proportion of your thrusters in the direction you want them.
To accommodate small ships and existing builds, it could work similar to the power system, where up to a certain thruster dimension, thrust increases omnidirectionally, and only after that would the actual orientation matter. So you always have some orthogonal thrust available, but if you want the optimum, you have to build it accordingly.
And if it is really such a staple of scyfi, then by all means, why not add dynamic thrust reconfiguration on top of that.