I agree that the datum line should be based off the crank holes as THAT is the item that your modifications are directly related. Datum off the pressure plate holes, as with the change in clocking, makes the entire process shot in the dark. Even if you are a little off, which drive me crazy as there should be base point, it's not likely to create an issue. JMO and the sentence below sums up some of this.

Balance tolerances on these factory setups was so poor, I doubt the drill cutting angle would make a material change in the acceptable range of error.

Just a guess here. There appears to be a locator hole in the pictured flywheel with the external balance reliefs. Does the flywheel in question have that locator. Bet it's on the datum line passing through the cranks centerline.

I'd prefer it to be spot on and for $100, wouldn't waste time on the process. Sell the current flywheel and buy a new one already balanced.