Try getting a 5 year old to understand that concept

The article did mention a great solution for Firefox. Checkboxes removed can still be options provided via addons like Matt mentioned, but this isn't fesaible for many other products.

Another solution is some sort of debug like console. The URL about:config for example in Firefox exposes tons more options. The same applies to Mac software that allows people to change stuff via a "defaults write" command. Windows works the same with it's registry. And most games do the same, though how accessible this remains to the end user varies wildly.