If I were to hazard a guess the actual registration process with a registration code should be fine. The problem with the PSN store is that Sony has the store designed to prevent people buying the same license twice (with good reason). It also prevents you buying 'DLC' for games you don't own. My guess is that the upgrade from PS3 to PS4 versions of the client didn't flag anything on the PSN store so it still thinks people own a PS3 client and never bought a PS4 version.
It's the PSN account that has incorrect purchase history flags in this case, not the Mogstation game account. With that in mind there shouldn't be any problems registering a physical key.
