The GPU can perform higher quality scaling, and doing it this way means there is no additional lag caused by going through the monitor's slower scaler.
I understand the nVidia GPU driver control panel has the same options... (I believe AMD's Catalyst control center also has similar funtionality, but is less intuitive than that of nVidia's). Although I'm unsure if Intel HD graphics control panel has those settings...
but personally, sometimes I like to adjust the screen without going thru the control panel (ie. using the monitor's built-in controls if it has one -- especially if one is already inside a game, and just want to check what it looks like if 1:1 or widescreen, etc. in case that game doesn't support the native resolution of the display). On a powerful graphics card, the GPU scaling probably does the trick...
Anyway, it's a personal preference, and probably won't matter to most other people (except me?)