The tall cones are tall because the whole threaded shaft of the button assembly screws tight to the bottom of the CP (sort of, there is the adjustment nut on the threaded neck...).
The short cones bolt to the CP and then the buttons screw up into them only as far as is necessary to clear the top of the cone.
The CP holes for the tall cones only have to be big enough for the neck of the button, the CP holes for the short cones have to be a larger diameter, because the short cones also have a neck that must go through the CP.
If you are trying to figure out which cone to use on a stock Atari CP, just stick a button neck in the hole and wiggle it. If there is a lot of play, it's meant to have short cones. If it's pretty tight, it's supposed to have tall cones.