When I make them for guns being done in house this is how I do it because that's how all my programming is done for the mills.
Since the bulk of "DIY" guys at home don't have access to this kind of stuff I altered my retail ones to where you just spot face the pillar hole with a spade bit or drill.
Performance wise it makes no difference. Seriously. These things have evolved over time and they started out with square heads. I left them that way cause I'm too lazy to go back and change all my programming. That's the only reason.
EDIT: I read your post again and I think I may have misunderstood you. The pillars don't key in the action at all. No, no, no doesn't work that way. The pillars have a single line point of contact with the receiver. This "stand off" is .050" to allow for a pad of bedding to go between the action and the base of the pillar. The raised "rib" is contoured to the action and prevents screws from crushing the stock while also providing actual bedding material contact. I feel this is much better as you get more of a 1:1 point of contact this way. The epoxy is going to mirror image whatever it contacts. If it were keyed it would act as a recoil lug and that is a big NO NO. Especially with repeaters using a floor detach magazine or hinged floor plate.
The whole idea behind this was to get away from pillars that end up with a skim layer of bedding that always flakes off later. It also acts as another mechanical lock to ensure the pillar never moves or comes loose. The real feature with the swelled head is that it controls the seating depth of the action. If done correctly it puts the receiver on the exact "waterline" of the stock's top edge. This means the barreled action is half in/half out and level with the stock.
Hope this helped.