Im sure now that the real Sebastian is in the closet. Will Tudor is what the real Sebastian looks like, so Jonathan has taken on Sebastian's appearance (in the same way that Valentine glamoured himself to look like Michael Wayland). Since they made a big deal about having cast Will Tudor, and I am sure he is meant to stay on the show, I am guessing he will be sticking around, which presumably means that after Sebastian is found out or reveals himself as Jonathan, he will continue to wear Sebastian's face.
I think you're right. The Sebastian we're seeing is what the real Sebastian looks like. Jonathan has glamoured himself.