For Swan and Dolphin - yes, even if you book directly through Marriott.com you can enter your Marriott provided reservation number and add it into
MDE which then allows you to make a Park Pass reservation for a resort. Thats the same way it works for Disney Springs hotels (but obviously not through Marriott since there are no Disney Springs Marriott hotels).
I wasn't sure about Flamingo Crossings though since they were added to Disney World Gateway hotels but it doesn't explicitly say they will get perks.