How to balance application for a faculty position between exceptional and ordinary?
One non-surprising way to help your application rise to the top is to have your advisor or another letter-writer contact a colleague they know at a school you're interested in and give you a good word in person (obviously not always an option). 

If you are really in the position where you are "too good," then you should follow the advice in the other thread you mentioned, and explicitly spell out in your cover letter why you want to work at a particular institution.