Not directly. Simply put, the leading edge of the board moves as much as the trailing edge, meaning the whole slot is a different shape. This has to do with loading the board correctly so that it jibes to the correct place in the case. The notch in the back of the case (as you describe it) simply creates space for carpet to fix the board in position. After you add the carpet the resulting gap is actually smaller and fixes the board in place. It's a simple approach to fitting a board into a hull, the production tolerances are greater resulting in cheaper production costs but the trade off that reduction in accuracy.
Just to be 100% clear I haven’t seen this notch in the NACRA case as you describe it. It sounds exactly the same as what Hobie has done in the wildcat and that is what I have described above.
Possibly the problems you are describing is why NACRA has moved away from the jibbing boards and chosen this new solution.