To me it would matter most what the crossbar spread distance was, and how much cantilevered over-hang on either end of the vehicle was presented, between a set of Yakima/Thule/etc on-cab racks and the spread on a set of raised crossbars off the bed rails. On the whole, for highway aerodynamics, I would prefer a couple extra feet of cantilevered canoe (red-flagged) stem hanging out behind the tailgate than several feet of bow unsupported out front.
The side windage and passing semi effect seems much more pronounced with the cantilever up front.
Some of the better bed rail rack systems are easy on/easy off, which is a prime consideration for me with any vehicle rack. I don’t need to be driving around 24/7 with roof rack rails, especially with crossbars wide enough to accommodate two canoes.
If I can remove the crossbars in a few seconds I am happier leaving the gunwales stops and belly lines in place on the (removed and stored away) crossbars. All I need do is slap the crossbars in place on a relatively clean roofline, with belly lines and gunwale stops already attached.
And, when I get to the launch, take those crossbars, gunwale stops and attached belly lines off the roof and store them inside the vehicle.
I may be pooh-poohing the hazard, but in normal (non 4WD crazy rock hopping) travel I really doubt there is enough twist between the bed rails and the cab roof to do any damage. The gap between the cab and bed walls on my truck is barely a finger width wide; not a lot of twisting gap before sheet metal cab crunches against sheet metal bed.
I would be tempted, with a Supercrew cab and 5.5 foot bed, to get a single cab roof crossbar and a single raised bedrail crossbar, pad the back crossbar with some split foam pipe insulation to accommodate any jiggle or twist and call it the longest spread I could possibly achieve. Crossbar distance matters.
I will know the consequence of that strategy eventually. The quick release Tracker II Thule crossbars on the Tacoma’s (above cab height, mid-rise) Leer cap are 44” apart and work well for two canoes, gunwales down between stops. This year I want to add a single (short as possible) Thule crossbar to the cab roof in hopes that, in occasional shuttle need, I could carry three canoes all gunwales down, two staged cantilevered back and the third on taper staged in between, held in front on a single cab roof crossbar.
I would need to add some raised (minicel) support to bring the cab roof crossbar up to the height of the mid-rise cap roof crossbars, but that padding should offset any minor flex between cab and cap/bed rails.
In any case, with a long Supercrew cab and 5.5 foot bed I would at least figure out something that presented easily removable crossbars that can accommodate two canoes. The advantages of being able to carry a second canoe on shuttles and friend trips is beyond measure.