Yes you can apply the discount. However if you have a package bundled with Tickets and the ticket price goes up, you pay more for the tickets.
But please remember (
@wannabeBelle drilled this into me) that the more guests who reserve their preferred resort and room type ahead of time at rack rates means that there is less likelihood that that specific resort and room type will be discounted when promotions are announced. Disney does not discount resort and room types that sell well.
Unless you want a very specific hard to score room type, it is never ever ever ever ever a good idea to book prior to promotions being announced.
As the most recent promotions show, Disney has conditioned their guests to expect discounts, even with SWGE opening.