For several reasons, I think that which way to load the flat of the ball is largely an academic question without much consequence.
Let's suppose that the flat edge of the ball is not loaded up or down but sideways. The flat only covers a small percentage of the surface of the ball's diameter. Let's estimate that as being 15%.
Then the ball is loaded and a ring of lead is shaved off all around the diameter, making the percentage of the diameter with the flat spot even smaller. Let's say the original 15% has now shrunk to 7%. That leaves 93% of the surface diameter of the ball unaffected by the flat.
Does that small 7% gap leave part of the ball unsupported when it travels down the barrel upon firing?
No, probably not. That's because the 93% of the surface of the ball that's unaltered is supporting it as it travels down the barrel. The other 7% that may still be flat doesn't matter at all.
I doubt that it even affects accuracy much at all, especially at relatively short pistol shooting distances.
This same type of flat spot occurance happens to .22 LR bullets when they enter a gun's chamber after being stripped from a magazine, and part of the outside diameter of the bullet will often get gouged by the sharp lower lip of the chamber. There's not much if any consquence unless if one is an Olympic shooter and is concerned about such a minute imperfection.
And pistol sights just aren't all that accurate to begin with to cause a person to notice any difference at all during shooting.
Also, I've had an air pistol match shooter tell me how he partially squished the skirt of .177 air gun pellets and then fired them through his match air pistol without noticing any accuracy difference at 10 meters. He said that his shots still landed inside the 9 ring which is the same accuracy average he shoots when using perfect & unsquished pellets.
So while the projectile's imperfections may matter at some point, for practical combat pistol shooting purposes it shouldn't matter at all what direction the round balls are loaded into the cylinder.
Just some food for thought.