So, there must have been a way to do smaller runs, at one time - lots of dairies had custom molded bottles.

If I wanted ~2.5-3 gal molded glass pails, would anyone know of someone who can do that? (The height and diameter are critical. The exact volume is flexible)

Many years ago Corning glass from New York would do that, they are into high tech stuff now. I wouldn't hesitate to email them and see if they could recommend someone.