You don't get FREE ground transfers or FREE Hyatt. They are loaded into the cost of the air fare.
In most cases, you can get a better price by booking the air on your own (as well as the transfers and Hyatt stay if desired). In addition, you will have MUCH more flexibility as to your flight arrangements. For instance, Delta used to have a direct flight from our home airport to MCO. This flight was NEVER used by DCL booked flights; they always routed us thru a connecting airport. This was a pain in terms of time, possibility of lost luggage, possibility of delayed flights, etc.
Yes, you can add DCL air up to 90 days ahead of the cruise, by which time you will have a good idea of what you can book on your own. You can also book the transfers and the Hyatt stay thru DCL is you wish; you can obviously make other arrangements to get to the port or spend the night.