between drilling a ball with a pin on axis drilling, and drilling a pancake cored ball that doesn’t flare to begin with?

If they used the same coverstock, the pancake core still flares, as much as 1 - 2"; their differential is in the .020" range. If drilled correctly, the pin in axis ball will not flare at all.

There's also the difference in the drilled RG, depending on, with the normal ball, what the actual RG is, and, with the pancake core, where you place the pin. The pancake cored ball normally has a high RG, in the 2.6 range.

So, both technically and practically speaking, there could be a huge difference between the 2 balls, again, IF they have the same coverstock. With different coverstocks, there's even more potential differences.

OK, then let me ask it this way.

 You have two balls. One is an old style, two piece construction, the other is an old style pancake core.
 You drill them to have the exact same flare potential, and they have the same cover stock.

 Any difference now?

 I’m thinking that there still would be.

The older ball with the real, dynamic core would, with pin on axis drill, have a much lower RG (pin axis is the lowest, as far as I know). So it would want to get into a roll much quicker than the pancake ball.