It's not just this ones better in the passing game and this ones better in the read. All qbs have certain tendencies and things they feel comfortable with. If one will tuck it and run at the first pressure then the D will not be so aggressive getting up the field. If one can extend the play then they may play more zone to be able to cover receivers for a longer period of time. One is a quick release guy, the other winds up. Lots of things for the D to prepare for other than just a different number under center.
If the coaches and players know who is starting, I'm ok with not knowing until the first play.