Why don't new flush valve seals have the same bump in them as the original?
The bump is most likely not necessary for a good seal.
Bumps like that are usually location devices for assembly (at the factory or on site). There's probably a corresponding dimple or slot on the hard parts of the toilet. They allow for quicker and more accurate manufacturing.
So just be sure that your new seal stays in the correct position as you tighten things up.