You want air to pass over with the least amount of resistance...
With it sticking out so far in front, it seems to be like 'pockets' that catch air...
Perhaps turning the boat over, so it sits right side up, allowing the air to flow across the bottom, such as water would, and flipping the kayak upside down, in the boat... This would allow the air to pass over with least resistance as boat bottom would be down and kayak bottom would be up, if you follow.
That is if you can do it without making it too tall... (Bridge clearance, trees and such...) and if you can secure it tightly like that...
They may fit together nicely, or they may not. Won't know until you try.
You may be able to couple boat and kayak together on the ground, then put it, as a unit, on the rack.
Also, if you can cover or tarp it (securely...) that might help as well.
Just giving you some thoughts...
Again, you want the air to flow and not get trapped in 'pockets'...
There is a reason why planes, rockets and such, have smooth exteriors without pockets/recesses that trap air...
Good luck!