We've only ever gotten park hoppers, so I don't know for sure if you can upgrade later. However, I do know that the tickets and room reservations are handled separately in My Disney Experience, and not as a package. The package booking confirmation number only links the hotel reservation to
MDE. A day or so after you book, Costco sends you an another email with a code to redeem your tickets on MDE independently of the room reservation. So my guess would be that Disney would treat the tickets as if you just purchased them separately, and you should be able to upgrade them to park hoppers directly through Disney like you would any other tickets. But again,
this is just my guess based on the fact the tickets and room reservation are linked separately, and I don't know for sure, so I would check with them to verify.