The answer is no, in terms of scoring. Once you submit your design report, your passenger capacity becomes a fixed number that cannot be changed with an ECR. If you submit your report with 16 passengers, for example, that number will always be the reference number used in the scoring equation. If you fly with fewer passengers, the empty seat penalty comes into play.
You are still allowed to physically change the number of seats in your aircraft after the design report. If you do so, you must submit an ECR and there will be a small penalty associated with the ECR. However, this ECR has no effect on your seating capacity number originally set in your design report, used for scoring. It only covers the physical changes you make to the aircraft, if it is different than the design report.