With my Tubus Logo rack, the rack stays have to go outside of my SKS fender stays because the fender is completely surrrounded by the rack. And isn't this true on all rack / fender set ups?

Rack bolts shear off, that's true, but if you don't overload the rack and use stainless steel bolts, it's hard to imagine that the extra couple of mm's from the fender stay will provide so much more torque on the dropout that the bolt will shear that much more easily. I've never worried about it and have had no mishaps.

If a bolt does shear off, you might be lucky enough to have a bit protruding enough that you can get a bite with vice grips. But it will likely shear off right at the bike frame and you'll need to improvise with zip ties instead. A sheared off bolt is usually remedied only by a machine shop.