In the Incredibles play set I have heard that you will be fighting Syndrome... Yet you can by Syndrome to use, so would Syndrome fight Syndrome if you got the figure?
yes. i don't remember what video it was but in incredibles video from where it was demoed at the reveal he said that if you chose to be syndrome in the play set story mode that syndrome would fight syndrome.
I think the playset experience will be the same but I expect there will be a small explanation as to why, even if it is only in the text dialogue on screen.