If I am reading correctly, there are nuts and bolts holding the inner LP tank mounts thats are in the way of the flooring. These are installed with the bolt entering from the bottom, and a nut on top?
If so, must be a difference in '08 + models. Mine had bolts inserted from the top, and nuts outside on the bottom. The rear one easily reachable from the wheelwell with a gearwrench..
OK, so lets say you have to install hex head bolts because the carriage bolt shoulders wont anchor.
If you have the bolt installed from the top, there will be a head and washer standing proud, and interfering with the flooring. After install, perhaps use a hand held angle grinder, and reduce the head thickness. 'Make' it a carriage bolt head. It may still be too high. My next step would be to hollow out the flooring on the back. This SHOULD be a very low traffic area, and the lack of support wont matter much. Use the same angle grinder, and carve away. Maybe test first on a scrap piece.

With either the nut or bolt head on top, instead of grinding the bolt/nut consider 'relieving' or routing out a shelf 1/4-3/8 of an inch into the floor. This will leave 1/2-3/8 " of plywood to support. Get a large fender washer, trace the outline, and use a router, chisel or other available tool to make the pocket to sink the nut/bolthead into. Then hollow out the floor as above, if necessary.
If you can somehow fit a nut on the BOTTOM of a bolt, maybe dont use a washer on top of the flooring. Tighten the heck out of the bottom nut until the head of the bolt sinks into the floor. Lube the bottom nut and washer to make things easier pulling the head into the wood. If the head doesnt go in far enough, hollow out the floor as above. I suppose this may work with a nut on top as well - Assemble things with just a nut on top of the flooring, no washer. Just have to trim off any excess thread.
For a thinner nut, try to get a 'Jam nut'. OR grind off 1/2 the nut. DO NOT round it off like a carriage bolt, unlike the head the nut is NOT attached to the center of the bolt.
Hope any of that helps!