Bottle neck cases that are rimmed, and head space on the rim, will still fail to go fully into the case, if the shoulder gets pushed out too far. In this case they are headspacing on the shoulder. This would be why those instructions were given with the dies.
The perfect way to set the sizing die is to fire, preferrably a new case, in your rifle. the shoulder will then be extended to the chamber shoulder. Now, if you neck size only, in a very few shots the shoulder will have expanded enough that you can't close the bolt.
Therefore, set the sizing die so it just kisses the shoulder of the case. That way it just keeps the shoulder from expanding further and will not shorten case life any more than just neck sizing.
The calibre where this is most important is the 303 British. The military didn't want anything, like mud, etc, to impede the 303 cartridge from going into the Lee Enfield. Therefore, they made the chambers nearly ¼ inch ahead of the shoulders on the shells. If the shoulders on these were pushed back with every reloading one would get mighty few reloadings from the cases.