My MB markers protrude just slightly over the surface. Since I don't track near the thumb hole, I don't worry.
Is yours rising more with each use?
As far as I know/think about it, it's the holder/marker of the mass bias on this core, even though the core has been changed to remove all of the MB strength and 99% of the RG differential.
I suspect you could sand it even, but if it protrudes more with use, I suspect yours came loose from the core. I'd worry about that a little.
Aside, I think that only on Brunswick made balls (MoRich) is the pin a cap or a marker. On most others, I believe is a plastic rod used to hold the core in place while the filler and the coverstock is poured. I've had those "caps" crack and the pieces fell out when I placed the pin exactly between the finger holes on Brunswick balls. On an older Columbia (messenger Ti Pearl) and Track and new Visionary (Gladiator Pearl), the pin didn't even crack.
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"None are so blind as those who will not see."