manual trans with 5.9 magnum

... My old gas 5.9 2500 HAD NO PILOT DRILLING with an automatic. You would have to either have the crank machined for a pilot, or hand drill a clearance hole for the pilot shaft, then use the large diameter pilot bearing/ fits in the pilot hole.
...

My 5.9 was drilled for a pilot bearing.
McLeod sells a 130 tooth flywheel that takes a bolt on weight for the mag balance....

Why are some drilled and some not? Is it only Magnums that were installed at the factory with a manual transmission that are drilled? How about Mopar crate engines?