I believe they just used good old standard lamp cord for all the connections light connections going to the penthouse top. I don't really know why, other than it would have more sheathing and maybe is a RVIA rule. I went with standard wires and split wire loom, I use
Flame Retardant Split Loom It is much better than the standard stuff at Home Depot. It can be found at standard marine shops.
If you are going outside the penthouse, make sure you make some room on your furring strip at the corners. If you plan on doing solar panels in the future you will want room for those also.
If you installed the brake light back the way it came (incoming wires facing up) I would think about drilling some weep hole in the bottom corners.
As you have found the power path is is via the fuse at the DS corner. The ground wire for the top lights will be attached to the van metal. SMB uses the van body for the ground return path in a lot of places. The positive side of the fuse is attached to the 10-Awg 30-amp passenger side circuit with crappy quick splices. So now is a good time to consider changes in that.
have fun
-greg