My thoughts but no solutions;
If the cab is solid mounted then welding the cage to the body makes more sense since the that will stiffen up the whole truck. From what I've seen on others trucks and cars with cages you will still have problems with sheet metal cracking. This may be because of the way metal changes when welded on; it gets more [?] brittle, leading to cracking? Stress relieving may be an option, but that would involve heating up the metal and I'm not sure how hot it would have to get. you would probably have to remove EVERYTHING that could melt. I would think that welding in that piece you drew would delay cracking though.
To late now, but if keeping the rubber body mounts, I would use the roofing gaskets that are used on metal roofs to seal around tubing protruding thru the roof. It has a flexible 'rubber' gasket that can be cut to the hole diameter that you need and the outer perimeter is made of metal that bends to conform with the profile of the roof. This would allow some movement between the body and cage/frame and still seal out moisture.
Richard