All the solutions here would result in direct conflict with the wording of the ability.
This makes sense because it wouldn't make sense to play a shapeshifter and invest in class levels sufficient to then learn the polymorph or wild shape spell, except for weak shapeshifters like Changelings...
May be a dead thread, but the wording is technically concisely taken care of in the term "instead". If the character has polymorph as a spell blah blah blah they gain multimorph INSTEAD blah blah. That means that whether or not they have both, the character gains multimorph INSTEAD if they have...