Rooftopping on truck topper/canopy/cap

I plan to transport my ski on my truck topper, which has tracks running the length of each side on top. The maximum crossbar spread achievable on the topper roof is about 53 inches, and the tracks allow shortening the crossbar span as desired. Crossbars are round Yakimas. The truck is a Nissan Frontier kingcab (extended cab, not a crewcab) with a 6-foot bed.

There are two options right now:

1.  Carry the ski upright and forward-facing in Spring Creek kayak cradles, which use pairs of flexible rubber pieces to cradle the boat. The spacing between each pair of rubber pieces can be adjusted to accommodate very narrow boats.

2.  Heavily pad the crossbars themselves with dense foam and carry the ski upside-down, either forward or backward.

a) If placed forward, the more pronounced lip at the front edge of the bucket would minimize slipping backward. But the ski would have more length overhanging the back of the topper this way.

b) If placed backward, the lip of the rear edge of the bucket is not so well-defined, but more of the ski’s length would extend over the truck cab. This part of the ski also is shallower, so it might be less interference with oncoming wind, though I don’t know if it makes much difference and anyway, the rudder on top sticks out.

The ski is a Nelo 520 S. Because I don’t have the ski itself yet, I don’t know all the measurements relevant to figuring out how to rooftop it. Nelo’s site gives ski length and width but not where the bucket begins and ends from each end of the ski, or how long the bucket is.

I’ve only seen one kayak rooftopped backwards and wonder if there is a good reason to avoid carrying the ski backwards, though I’ve also seen rowing shells transported facing backwards. The only reason I know of to avoid it is superstitition.

I don't like placing my ski backwards, mainly because of the rudder, but I am sure all your proposed solutions would work just fine. Just don't put the boat too much forward, this would make it wind sensitive - the strongest force on the boat is wind from the side. This will not be a big issue with a Nelo 520, though.

When carrying the ski upright, the foot straps, leash, seat pad. etc. are all subject to UV damage. If the ski is transported with the tail facing forward (backwards) I strongly suggest securing or removing the rudder to prevent it from flopping around in the wind and causing damage. Other than that suggest you do what works best for you. May take some trial and error to figure it out. 
 For me I place the nose of the ski up on my racks from the rear of my full size van and slide it all the way forward. I then roll the ski up side down on to simple v shaped foam pads or pool noodles while standing on the rear bumper. Slides better when the ski or pads are wet. I lash it down with rope secured to dock cleats. It is just real simple and been working well for me for decades. Many people prefer and are more comfortable with much more elaborate options. To each his own. 
 Just thought that I would add that in real windy conditions, and you are by yourself, having your vehicle pointed downwind (parallel to the wind) makes the rear loading technique quite handy.