How to balance application for a faculty position between exceptional and ordinary? Following the opposite factors described in answers to the question What makes securing faculty positions difficult?, I came to conclusion that an application for an academic position should be balanced. It is understandable that there is a high competition for faculty positions, and a qualified applicant may be not even invited for interview; thus, everyone tries to even overestimate his/her achievements.

However, the interesting points in answers to the above-mentioned question was that too good application might scare the committee, then preferring not to take a risk. Thus, an exceptional application will be simply ignored.

In addition to obvious evidences in the CV, how to highlight exceptional features in the cover letter? For example, potential research achievements, which are not obvious in the CV, promising plans, etc.

Or the strategy must be in this direction to convince the committee that this superstar applicant is a good chance for your department!
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.