Flush is not correct. Seated so the anvil is in contact with the bottom of the primer pocket is. This may mean the primer face is a few thou in depending upon the brand of primer and the depth of the primer pocket. Teach the tip of your finger to measure this after each primer is seated.
Not having the anvil in contact with bottom of the pocket risks misfires.
I actually preload mine about 1 1/2 thou using a 21st Century tool. Difficult to do that using a press or most hand held tools.
Usually primers get seated too deep/are partially crushed by press priming.
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