I think generally Universal doesn't require you to get the tickets as a package in order to take advantage of their various hotel deals (like the food gift card or the "stay more save more" discount).
Also the packages are much more difficult to change/cancel vs booking the room separately. However, with the packages, if you do cancel, the attached tickets are refunded - otherwise tickets are non-refundable (but are generally changeable if you call, or they retain their value if unused).