I uniform the flash hole and primer pockets in all new brass or at least all brass that is new to me. That way I know all my brass are equal on that account.

Cleaning the pockets is important, at least to some extent. If you have too much build up in them it may keep you from seating the new primer fully. This could lead toproblems from poor ignition to the dreaded "Slam-fire" in a semi-auto rifle that has a floating firing pin. You don't have to get anal about it, but getting most of the crud out of the pocket is definitely to your advantage.