You are being picky about a detail the builder may have barely given a second thought to. That the track ends (track bikes have track ends, not dropouts which open to the front or down) are exactly parallel and line up so an axle through them is square with the frame and not trying to bend when the nuts are tight is important. That the ends of the slots line up? That only matters when the wheel is pushed all the way forward, a position never used on the track (except to slacken the chain so you can drop it off the cog and pull out the wheel). The bike is never ridden that way. (You would have to use a chain tool to remove the wheel.)

On a vertical dropout road bike, that detail is crucial but not here. If it really bugs you, I suppose you could put a wheel in. push it all the way forward, snug up just the nut on the side that hits first, pull off the other nut, center the tire and measure the gap forward of the axle, then file down the other dropout that amount. I wouldn't but most track bikes have plenty of material there.

Ben