If you book a package through Walt Disney travel, you will purchase everything together on the first call, you will leave a deposit and then be required to pay the remaining balance by a due date, there is a cancellation fee charged if you cancel or change your package. Once you pay your remaining balance and sometime befor your arrival date, usually three weeks, they will send you a package with the luggage tags in it. When you check in they will give you an envelope with your tickets in it and vouchers to go to the travel company and pick up your pins.
If you make a room reservation only through Walt Disney you are required to pay one nights deposit at booking and you pay the remainder when you check in, if you cancel within five days your money is returned. You can also purchase your tickets at the hotel but you will not get the vouchers for the extras.
So it's not really so much who you booked with, it's more how it was priced and paid for. Someone who has an AP for example would most likely book a room only because the wouldn't need tickets. We never book the packages because they always cost more than getting everything separate.
And just as an FYI....they really aren't freebies, the cost has been included in your package price.