I was just looking for answers to this same question of mine (different wall fills and plan & section) and am discouraged to hear that I must also resort to 2D fills in section. I will add to wish list if not already there.
Practically speaking I guess the way it would work would be that the override fill must occur on the purely symbolic plan, whilst a section is a 'true' representation of what is actually modelled and therefore must display the fill representing the actual material.
I'm just thinking out loud, but would an extra 'overlay' fill on the section solve the problem better? i.e. Display the original material fill on both plan and section, but have an extra fill with an adjustable origin that could be used to display the coursing. I don't quite know what would happen with irregular courses or junctions with floors, mind you, but that would have to be sorted out with the original wish also!
I am now coming to the belief that the goal is to draft a little as possible and keep true to a live model as much as possible. This way changes are updated to the live model. Redundant drafting of fill overlays is a waste of time and makes for one more thing to remember when a change is made elsewhere. How many other things that we draft can GS incorporate into the model functionality gracefully?