Why is the “Default extrusion width” when set as a percentage, a percentage of the layer height? Wouldn’t it make more sense to make this a percentage of the nozzle diameter?
I’m not a slic3r expert nor very knowledgeable about slicer algorithms but it seems logical to relate it to layer height because that’s what you configure for your layers. In an ideal (round) world, a layer height of x produces a layer width of x (actually it’s linearly related to x, because it’s more like an elipse), even when the nozzle is wider. The slicer tries to accomplish this by extruding exactly the amount of filament to get the desired diameter. So, it seems only logical that if you want a wider line, you need to dial relative to layer height, since that varies, not the nozzle diameter.
And, on a sidenote: I do believe Alessandro and Joseph think a LOT when coming up with slicer algorithms and ideas. Just check their brainstorms on the issues list 
The printer will not print right if the width requested is less than the nozzle width. As stated elsewhere in their documentation, the width should be between 100% and 150% of the nozzle width. Certainly, the amount of plastic varies with the layer hight, and the software compensates for that, but I don’t see any reason to vary the width of the print stream based on the layer height.
If one prints with a layer height of 0.4 mm on a 0.5 mm nozzle one would expect to print with a width of 0.525 mm, or 131.25% of layer height. Then if the layer height changed to 0.2 mm the width would become 0.2625 mm which is too small for the nozzle.
I suggest you take this up with Allesandro and Joseph: https://github.com/alexrj/Slic3r/issues. We certainly can’t help you here.