I was also confused as you are. The top plate covers just the very top of the mech. The shifter bolt is inside the piece your tring to remove. This very same thing happened to me a couple of weeks ago. I also removed the very top cover. And I like you thought the shifter bolt was in there. Its not.
Since its stuck in a gear your going to have to wiggle, turn, shake, twist the thing out. Its alot easier with the top trans mount removed. Mine was stuck in 3rd so I had to angle the tower and twist. It took a few times but it did come out.
Heres a pic of a broken shifter bolt