Workaround: divide 96 by logical DPI and then multiply that with the width and height of the resolution before calling Screen.SetResolution:

var width = 1920;
var height = 1080;
var dpiMultiplier = 96.0 / logicalDPI;

Screen.SetResolution((int)(width * dpiMultiplier), (int)(height * dpiMultiplier), false);

This bug does not manifest when setting resolution for fullscreen mode (when the last argument is true).

You can obtain logical DPI using this windows API:

https://msdn.microsoft.com/en-us/library/windows.graphics.display.displayinformation.logicaldpi.aspx?f=255&MSPPError=-2147217396