In Top Bar Hives, some put the entrance on the side of the hive making it like in Langstroth where the flight path would be parrallel to the combs; others, placing the entrance on one end, when entering, bees face a comb.
In nature, hollow trees and cavity, my observation has been this latest format (combs -more or less- perpendicular to entrance)
Obviously bees will adapt (as in Langstroth hives) to a different position of their combs.