This is a quote from Better-Bottle's website with regard to attempting to drill your own port in an unported Better-Bottle. I don't believe that the holes are drilled out in the factory. They are most likely punched out when they are forming the bottle.
Do not attempt to drill ports in unported Better-Bottle carboys, because the special PET from which the carboys are made is very tough and specialized tools are required to make sufficiently smooth holes.