What dimension does this b reflex port length refer to?

There is really no way to tell unless you had a drawing showing the port length in the cablnet. However, if the port length is computed acoustically, that length refers to the entire length of the tube, even if part of it is inside the cabinet walls. I would cut the tube to 90mm and 78 mm would protrude into the cabinet. Acoustically it is the internal length of the tube that matters, not how far it extends into the cabinet.