Depends on the core. Principally, drilling holes into ball markings does not mean anything special. These are just markings, and if you want a specific reaction, drilling. e. g. a finger hole into the pin might just be necessary because any other position would not do the job.
But back to the topic: placing the MB/PSA marker onto the thumb hole can be a tactic for asymmetric core balls if you want to achieve a hook/set recation. On symmetric balls or aballs with a low MB rating, you place the MB at 135° from PAP to create this reaction - somewhere close or even on your track on the negative ball side. It tames down the back end reaction, pronounced midlane recovery and is generally a nice control drilling, especially for medium-dry shots.
On strong asymmetrical balls, like the Zone Classic, this PSA placement can cause flaring problems (especially for high trackers), even create reverse flare! To avoid this, the MB should not be place further to the negative side of the ball than the thumb hole area.
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DizzyFugu --- Reporting from Germany
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