I agree it makes sense to take meat off the bottom of the dropout slot (if possible) to ensure correct alignment. However, in my case, I'm going to have to spread the dropouts/rear stays quite a bit in order to get the rear hub in. This Dyno frame has alot more material on the topside of the dropout slot so I think I will have to remove from that area.
In theory, the axle should be resting on the top surface of the dropout, and not rely on the clamping force of the axle nut to hold the wheel in place vertically.
I agree with Bairdco that it you cut straight it shouldn't be an issue either way. You'd have to be way off on your cuts to make an appreciable difference.