Hey Vic,
I'm attaching a photo from when I did my roof rebuild for clarity. I'm with WS about concern if two screws through the 1" square tubing on each side, (if you couldn't use bolts and backing plate) would be sufficiently strong for either weight as downward stress, or more importantly, for upward lift, of things you might haul on the racks, like a canoe. Also the wide body artificial rain gutter mount with four holes might not be feasible with one inch tubing, as the holes might be too wide, even though it would then give you four screws per side, which does seem stronger. The side tube along the perimeter of the roof is not all that rigid either, having seen the flex in it when everything is uncovered and bare. I have a set of those same Yakima gutter mounts and the regular two hole artificial gutters, but chose not to attempt it for fear it might pull out when loaded.
The Yakima tracks FWC installs, have screws about every 5-6 inches, and might have better strength/ stability with accompanying control towers, and I know some have utilized them for hauling canoes and kayaks with success. I might just be worrying about bad possibilities too much, and your thought to use gutter mounts might be fine, I don't know.
Your other question about using a backing plate, with bolts and nuts, on the other side of the one inch tube would certainly be stronger, but the only way I could see doing that would be to cut a slot on the headliner to allow you to get a plate and nuts in there. The headliner is tucked up and around the outer tube, and the outside trim ring is screwed down so as not to let you pull the headliner down to work on things. If I recall correctly, Sqatch used mounts on top, and used a backing plate on the inside of the roof, with mounting bolts coming through the roof struts and through the headliner with a backing plate and nut exposed on the ceiling.
Anyhow, sorry for the long response, just thinking out loud.
Good luck with whatever you decide, I'm still trying to figure something out myself.
Poky