I have been pulled over by the cops countless times and more often than not, they had nothing on me. They pull folks over for the lamest reasons.
My guess is that your breath-analyzer did not register you as being drunk or perhaps borderline, but since you admitted to a few brewskys, the cop wants to make sure you don't go off and smash into something minutes after he lets you go.
In other words, the cop is covering his own a$$. He doesn't have enough to ticket you but wants to avoid his superior jumping all over him should you go off the road and hit something or somebody. You could have gone on your merry way and not worried about it because he had nothing on you in the first place. At least in my opinion.
Chances are since you did register a low blood alcohol level, he wanted you to wait a while while the remainder of the alcohol dispersed from your system. He could not have pursued a later arrest because you were not guilty of anything.
There's possibly a lesser charge for Impaired Driving, which may have applied in your situation, but he would have been in serious trouble to have let you go, when in his opinion you were not fit to drive. What if you had an accident on the way home? He would have some sort of contributory negligence in the accident.
In my opinion he was bluffing, but you probably did the safe thing.