You cringe if you saw them doing it at the factory.

Drive them in with a big hammer.

LTG

Nope. The factory simply smashes them in. Under a pop bumper, I hammer them close, then use a nail set or similar to punch them down the rest of the way. Try to minimize PF flex.

An exception would be the same twist speaker screws used on Monster Bash to hold the Drac motor assembly. Since at least one head is really, really close to an insert, you would not want to fracture the wood there, yet the screw needs to be flush as it is not hidden by a pop bumper skirt.
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Chris Hibler - CARGPB #31
http://www.Team-EM.com
http://webpages.charter.net/chibler/Pinball.htm
http://www.PinWiki.com - The new place for pinball repair info

could you use a brad point drill bit the size of the head of the sss with some sort of stop on the drill bit to prevent it from countersinking further than 1 mm?

Either a hammer and a drift punch, or if you dont want to pound on it take a drill motor with a deep socket and draw it down from the other side with a free running nut and a couple of washers