Thanks, Jason B, for explaining about the radius between shank and head of a socket cap screw. I have just measured the inner diameter of the flat on the underside of the head on a good-quality M5 stainless screw and it is 5.36mm, which explains everything.
My ' version of reality', as regards recommended clearance sizes, comes from the widely-used 'Zeus' precision tables. I now understand that this clearance size for the screw is less than the hole size needed to accommodate the radius on the base of the screw head, which is more likely to be cast than formed with precision.
Thanks to all the advisors who weighed in on this!