Scott, is the way you're reading the Standards here (that God normally regenerates at baptism) the typical, historical way this has been understood? I am sure there are PB threads on it (seems like there was one not long ago) but I don't have time to research.
I haven't read ch. 28 1. and 6. as speaking
to regeneration at baptism, but as saying that the efficacy of baptism lies in its right use, which would be pursuing holiness as a baptized covenant member in the fear of the Lord.