I can see that being a problem. But the fact is that by the time you are dry hopping, or transfering, there is so much alcohol content in the beer, its not a great place for bacteria to live. Otherwise there would be a need to sanitize the hops before dry hopping. How much dust, dirt and micro buggies are on the outside of the hop pellets? Or even worse, whole cones?
The alcohol helps kill most of the bugs on dry hops - that why we dont worry about it too much.
I spray the inside of my conical down with starsan and seal it back up, then mill grains within 5 feet of it. I've NEVER had a problem. Probably because I'm a business major, not a microbiology major...
When it's time to pump the wort into the conical and pitch yeast, I'll dump the collected starsan out of the dump valve and pump the wort into the conical via the racking arm, all sealed up except the blow off vent. I open the top of the conical up to run an O2 stone and to pitch the yeast, and then it's sealed up for a few weeks. All within five feet of where I milled the grain.