Since most of the bullets that I am seating are SWC's I drill out the cup portion of the seating stem until the leading edge of the cup rests on the shoulder of the SWC bullet. The bullet nose does not actually come in contact with the seating stem's cup. The shoulder is, hopefully paralelle the base of the bullet so it should seat square in the case.
With my flat nosed rifle bullets I use a seating stem that has no cup portion, it's just a blank. The flat portion of the bullet contacts the flat portion of the stem.
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