Rudi brought up a good point. Assuming the dropouts are perfectly aligned to keep the wheel centered laterally between the chainstays, if you file the leading edge (front edge) of the DO, the wheel will point to the left. If you file the trailing (rear) edge of the DO, the wheel will point to the right. Theoretically, both edges should be filed equally to maintain axle alignment (assuming the axle fits snugly within the DO). A tiny amount of filing might not sound like a lot, but when you do the math, that can cause the tire's lateral position be several mm between the chainstays. By my rough calculations, for each 1mm you move the axle longitudinally in one dropout, it will cause the tire to move laterally by 5mm. (axle = 126mm. wheel diameter = 630. 630/126=5).

When you have horizontal DOs, this is all moot because you judge how centered the wheel is by eyeballing the tire between the chainstays (at least that's how I do it) and the horizontal DOs provide infinite adjustment for that. But with vertical dropouts, that parameter is non-adjustable. Therefore the dropouts have to be very carefully aligned to keep the wheel centered.

However, if I file 0.5mm off of the axle (on both edges, to be symmetrical), I won't even be removing any of the core metal, only the threads. That shouldn't affect the structural integrity of the axle, should it? Maybe I need another cup of coffee before I think about that one!