Well it seems like the overall verdict is that drilling/tapping the dropouts and using a good amount of grease shouldn't cause me any problems, but proceed with caution. Maybe the boss man was just trying to be a know it all about the rust/corrosion issue. In situations where there isn't drilling in the seat stays (but there is drilling already on the dropouts) for a rack and I don't feel like using clamps, I've had great luck attaching the two braces from the rack to both sides of the quick release.
A user explained that the tubes are already rusting/corroding inside because they're not sealed. Can someone briefly elaborate on that? Why isn't ChroMo sealed from the elements?