The AMD uninstaller does it if you tell it to uninstall everything, instead of just telling it to uninstall the graphics drivers. It should be obvious that uninstalling all your low-level motherboard drivers could cause problems, and there is a warning to that effect that you have to click through.
However, having said that, if you check on the Catalyst uninstall instructions that are linked from the Catalyst download page, AMD do give instructions that say to uninstall all drivers, so customers can hardly be blamed for following the steps given by AMD if they don't know better. I do believe those instructions are wrong and take the user down the "uninstall all AMD software" path, instead of "uninstall AMD graphics software" that exists in the same uninstallation utility.
I can only think that AMD have some reason for wanting the user to get rid of all previously installed AMD software, but haven't thought what that can mean for users with other, non-graphics low level drivers from AMD.