I don't know how they are fixed on the blade, but Brad wrote me that it is almost impossible to remove them without proper tools.
With EdgePro Apex, the thumb studs don't really interfere the operation.
However, I hit a thumb stud with a stone when I tried to reduce the edge angle to 13 degree.
So if you want to go down to that kind of low edge angles, they may get in the way.
And I would imagine that the chance of scratching them would be higher with a bench stone, if not protected.
Hope this helps.
Miso