This is a phrase used to describe the arithmetic difference between two percentages. In football, percentages are typically calculated for third and fourth down conversion rates, field goal distance success rates, extra point and two point conversion success rates, and probability of scoring from a given position. When a coach must make a decision on what type of play to call, they will often determine the difference between the two percentages of success for the choice they have. For example, a coach may ask an assistant, "How many percentage points between going for it on fourth down vs. our ability to stop the defense?"
This is not an official National Football League measure, however the league does use these percentages for publicity and other efforts. This phrase is mainly used behind the scenes by coaches, team officials, and sometimes players and fans. Usually, players and fans are more concerned with action on the field to determine percentages of plays. Coaches need this data in order to make the best decision on the field.