I think the real question is why Nikon has given us 4 shooting menus and 4 custom settings menu that we can set for our own preferences, but does not allow us to store them as a default?
As an example, you set up a custom setting bank with your personalized settings for a type of shooting that you do, whether it's sports or flash, etc. Then you go on that shoot and you find that need to adjust several of the settings for this particular days needs. Later, when you want to reset the settings back to the way you originally had it set up you have to go through and reset the settings individually, OR you reset to "FACTORY DEFAULT" and start all over again.
Nikon should have given us other choices. When you set up a custom bank you should have a choice to "SET CURRENT SETTINGS TO USER DEFAULT", so in the above situation where you have changed some settings and want to return to your user defined presets you would choose for that bank "RESTORE TO USER DEFAULT", or, if you wanted you could choose the only choice we now have 'RESTORE TO FACTORY DEFAULT"