Yes. Guest staying at the Walt Disney World resort hotels can still take advantage of the
90 + 10 day perk when making their dining reservation online. To do this, you start by going to the main WDW website page of the first restaurant you want to make a reservation at. For example,
THIS is the page for Boma. On the left, you'll see a button that says "Make a Reservation." Click there and you'll find
THIS page. At the top there, you'll see a box that says "Update Your Profile" and a sentence that reads "Do you have a resort reservation for the same days for which you're making dining reservations? If so, please retrieve your reservations." Retrieving your reservation will allow you to link your dining reservations to your resort stay and will activate the 90 + 10 option.
You should be aware that there are still a few kinks in the system. The online dining site is currently only recognizing resort confirmation numbers made through Disney proper. It is not accepting resort confirmation numbers generated by travel agencies and the Disney Vacation Club. Disney is aware of the problem and is working on it. In the meantime, those guests can still use the 90 + 10 booking option, but they'll have to do so over the phone.