Don't know if it would work, only tried portrait mode once, yep the instruments moved around. It should work because you can save instruments where you want them in its placeholders.
There is an option to save your instruments as different 'options' or names. I would try moving the instruments the way you want in one orientation, then save as a different name, such as Instruments P1 for portrait, ect.
You will have to load the instruments when you change orientation.