@dfleis so i jost got going to test this problem since my own 2013-ish MacBook Air is fucked up real good.
So: I started in 16.04 and got 2 xrandr reports which both were in check but than i set the resolution of my LG to native and not 1440x900 (Laptop res) everything crashed.
I've updated from 16.04 to 16.10 (always with gnome) and I still have the same issue with the default image being scaled far too large. In fact, I see no difference than before.
Furthermore, the display wasn't even detected unless I used the xrandr commands I had to used in 16.04.
and changed the scale factor to my desired 1.5x1.5. For some reason running the script once leaves a portion of my lower display on the upper display (much like the image linked earlier), but running it twice ends up almost perfect!
I say almost perfect because 1) this is started to become a fairly janky solution and 2) after running the script my cursor will begin to flickering on my tower (main) laptop display but not the upper 2560x1440 external display.