I think I can explain. You are correct that having a passport is proof positive you are naturalized or a born citizen. The purpose of the birth certificate rule, in my opinion, is that is a convenient source of revenue for the government. I don't think it has anything to do with stupidity. I think it is part of a long standing government practice of collecting fees for services of little or no value to the citizenry.
The need for a birth certificate added another day to the passport renewal process. Note to Dominicans who like to make up stupid regulations. If you have a passport, you already proved you had been born in the DR or were naturalized. But yet again, a new legalized birth certificate is required to renew a passport. Stupid is as stupid does. Go ahead and link the Cedula data base to the new and amazing digital passport data base and to the even more incredible digital birth certificate data base and don't waste peoples time.