Filing the axle creates a stress riser that could lead to a failure. Opening the fork up, not so much. Granted, it will probably not likely be an issue, but I wouldn't do it just on principle. There probably is a reason that the industry moved to a larger standard size. That, and I'd imagine a front axle failure could be, um, eventful...
Not sure at all, but, Ive worked with a lot of different kinds of steel through the years and the new, bigger dia. axles dont seen to be as good a steel as the old ones. My guess (and guess it is) is that the lower quality, but bigger dia. probably about equals the older, small dia. 'better' steel. Im inclined to open up the dropouts if needed.