Hmmm, looked at the picks you have of the frame. Seems there are a few rust holes, but from the pics none really appeared to me to be so big as to cause any concern based on there location. If you have access to a welder, they are simple enough to fix, providing the damage doesnt stretch more than 1/3 the tubes diameter, in which case a patch welded over it would fix it up fine. The frames on these bike (like any other metal things) will rust faster in areas where the come into contact with other bits that help hold moisture there and provide a bit of mechanical agitation.
If it were me (and I had similar spots on my GL1000 frame that when investigated turned out to be non issues) I would patch up any problem holes like this, even if just for looks and to keep the tubes inside isolated. Since the frame is naked (and appears primed) it wouldnt mess you up to bad to do some welding fixes and re-priming. I would see if you can find someone that can weld AND knows about metal structures to see if there are actually worse than they look, but from the pics it looks far more stable than some bikes on the road I have seen (where people weld tubing on and cut the frame in spots).