I use Thule H2Go cradles on Thule cross bars on my Honda Accord. The only reason I use their cradles is that I'm too lazy to make my own custom cradles. I can't see any reason not to put the CLC boats on their sides in custom cradles. You can get more boats on one vehicle that way. Even with a 48" crossbar you ought to be able to get two 24" boats on top because the cradles can overlap the end of the bars and they don't need to extend to the maximum beam of the boats. I often transport my CLC boats with the adjustable cradles flattened out and contacting the boat only on the bottom panels.

I also have longer than recomended crossbars on my car. (I think they're 58") The shop that sold them to me was out of the recommended size and said I should cut them down or at least put red tennis balls over the ends to reduce the chances of someone hitting their heads on the bar getting out of the car. I left the bars full width and sometimes carry two boats in the cradles and my Patuxent on the crossbar on it's side in the middle. I have never hit my head on the crossbars.