Hi all!
I need some advice regarding transporting a canoe on top of a vehicle.
We have a 17’ tandem canoe (OT Penobscot) with bow and stern thwarts and a center portage yoke. We have a roof rack on the car, with cross bars adjusted so that they fall almost directly under the bow and stern thwarts. That is where I strap it down.
We also have a roof bag for traveling with our camping gear. If I nest it in between the cross bars on the roof, I can load it up and still fit the canoe over top. However, in order to do so, I have to remove the center portage yoke.
Is it ok to do this while traveling, or am I risking some kind of damage to the canoe?
We are going on a cross country road trip soon and I would like the boat to survive 
Don’t see why not. If you were strapping down closer to the middle, it might be a concern, but the thwarts are going to keep the straps from squeezing the hull too much so there is not much chance of slippage . I would replace the nuts on the wing nuts to aid in the removal.
I’m far from an expert, but I’m someone that just permanently removed his center yoke from my OT guide 147 to make it into a solo canoe. So I have an open area about like what you are suggesting and I’m doing that on the water without any issues.
For just transporting I don’t think you have any worries.
You may have a hard time placing it down over something like that though. Depends on how high your rack is and what your reach is and how strong you are with getting it up and over. My guide 147 is all I want to just slide it over into place. 
Find out what the weight limit is for your roof. I would be more worried about that than the boat or the gear.