Why do games only allow certain resolutions?
Note that in your Dark Souls example, all the resolutions listed are the exact same aspect ratio.  So the question is, why doesn't it support arbitrary aspect ratios?  

The answer is that it costs time and effort to support arbitrary aspect ratios, and if that money spent doesn't translate to increased profit, then it doesn't make sense to do.


This answer covers the 2d layout issues, which includes extra time and effort to create a versatile layout that can be resized so that elements do not overlap, stretch, or pixelate in an undesired manner, and that the overal UI maintains the best user experience.
The developer would have to ensure that the window doesn't get too large or too small.  Does it make the game any better if the user can drag the window size to be smaller than 800 x 450?  probably not.
you have to define the behavior of the camera when the aspect ratio changes. 


For example, take the following scene:



If we allow the user to change the horizontal size, we can decide to "zoom out" horizontally so that the same area still shows up horzontally but now we can see more vertically.



Or, instead, we can keep the same zoom level but just clip the viewing area more:



Note, that if you don't specifically handle the changing aspect ratio, the default graphics pipeline behavior will be to stretch the image:



These decisions take time and effort to design, code and test, but management has to decide if it actually makes the user experience better enough to be worth the time.  Apparently, most games have decided its not worth the effort.  I'd even go further and suggest that allowing users to screw up the best layout of the game is a bad feature.