Regardless of the reason why it's designed that way, I wasn't thrilled. While reading another post on this forum recently, I learned about the pen display trays from gopens.com. These are flocked plastic trays, available in several colors. (I used the tan.) The plastic is durable, but thin enough to cut with an Xacto knife, which is just what I've done:

Now I can put 12 pens in there, the right direction. Actually, the case is a little too narrow to allow a proper 12-pen arrangement, which is why the burgundy pen on the right crowds into its black neighbor's space. I tried cutting for 11 pens to start with, but that left gaps to the side. If you didn't need 12 slots, you could instead cut along the troughs instead of the crests, leaving 10 usable slots, with about 1/4 of a slot to each side. I expect that would look good, too. One tray is enough material to fill this case more than 4 times over, so you can experiment.
I didn't need to use any adhesive or anything like that. Because of the soft material used to line the case, you can just cut it ever so slightly large, and press it down into the case, and let the lining hold the tray in place.
If you were more adventurous than I, you could remove the separators inside the case, allowing you to put in 2 trays, for 20-24 pens. Given a choice between more storage space and a possibility that I'd wreck the case, I chose in favor of less space.