We've been to Scrub Island twice and booked the room upgrade when making our reservations and that is what I would recommend to ensure you get the type of room you desired. We wanted a Suite with a full kitchen so we could cook our meals with fresh fish caught around the area. Building 17 has the best views of the Caribbean and sunsets over Pusser Cay.
I don't think you get free breakfasts at the resort, but you might want to call the toll free number and ask to speak to someone at the property to inquire. They have a very good deli on the ground floor by the scuba/fishing boats that has some breakfast items as well as good sandwiches if you don't want to eat at the pool side restaurant Tierra Tierra.
Scrub Island is incredible and we can't wait to return.
SO! The property is a resort, which means that the normal Gold benefits, like free breakfast, will not apply. You can, however, definitely get an room upgrade if they have the availability. Here's a bit more info in case you're interested:
Hope that helps, bjones8162! Let me know if you have any other questions.