The reason is because with msconfig and Hardware Profiles, you can disable services that may be vital to boot your system. With the management console (services.msc) you cannot. Also, msconfig, while unchecking the box, is disabling the service.
The "Disable All" button also scares me. It should not even be there as no reason exists to justify disabling "everything."
Not "allowing" people to use msconfig reduces the flames and technical support questions in my inbox from people that fail to read the descriptions I offer with each service and the warnings I attach to them.