I've had a couple old horizontal dropout bikes that seemed to have a small vertical difference between the dropouts, so that the rear wheel didn't seem aligned vertically with the seat tube when centered between the chainstays.
I was just wondering, if the wheels are parallel with eachother and the bike, as if looking down on it from above, but have a small sideways offset or vertical tilt, would those affect the way it rides or tracks? If you're fiddling around with wheel position in horizontal dropouts and test riding for feel regardless of how it looks, it seems like the main effect would come from how straight the wheel is front to back, not whether it's off center or tilted. I think it's worth trying to fix if possible, just wondering if it might not necessarily be a functional problem.
If it's just a small amount, you could also maybe file down the threads off the axle at one spot instead of the dropout, and mark it's orientation.