According to Rabenu Yona (Sharei Teshuvah 3 9) that the reward for not doing an avairah is having done the mitzvah of Yiras Shomiam, why isn't every עשה דוחה לא תעשה, truly an עשה דוחה לא תעשה ועשה? I know that the Seforim ask the question, but cannot remember which ones
You don't automatically fulfill yir'as HaShem for every sin you are not doing. As is strongly and repeatedly implied in your cited passage from Sha'arei T'shuva, yir'as HaShem is an obligation on a person to avoid doing a sin when he would otherwise be tempted and have the opportunity to do it. As such, yir'as HaShem is not an עשה intrinsic to every לא תעשה.