Adding to the spline engagement by shifting the hub or adding to the hub making its center even further towards the engine would simply increase the local loading. Ideally the clutch flex plate should be centered (longitudinally) on the hub to more equally spread the radial load caused by misalignment.
It would be better though to simply have less misalignment through better manufacturing and assembly control - something many trouble free bikes seem to already have.
Error-compensating alignment spools would be quite easy to make. The problem is documenting the misalignment in the field, then communicating & getting the correct spools oriented correctly on reassembly.