Ubuntu overlapping displays while scaling dual monitor setup

Today, again I wanted to change my screen's display size, in my Ubuntu 14.04. This time I have a dual monitor setup and I tried all the commands I mentioned in my blog post Ubuntu scaling the display (Zooming).

➜  ~  xrandr
Screen 0: minimum 8 x 8, current 2560 x 1024, maximum 16384 x 16384
VGA-0 connected 1280x1024+1280+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
LVDS-0 connected (normal left inverted right x axis y axis)
    1600x900       60.0 +   40.0  
DP-0 connected primary 1280x1024+0+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
DP-1 disconnected (normal left inverted right x axis y axis)
HDMI-0 disconnected (normal left inverted right x axis y axis)
DP-2 disconnected (normal left inverted right x axis y axis)
DP-3 disconnected (normal left inverted right x axis y axis)
➜  ~  xrandr --output DP-0 --scale 1.25x1.25
➜  ~  xrandr --output VGA-0 --scale 1.25x1.25
➜  ~  xrandr
Screen 0: minimum 8 x 8, current 2880 x 1280, maximum 16384 x 16384
VGA-0 connected 1600x1280+1280+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
LVDS-0 connected (normal left inverted right x axis y axis)
    1600x900       60.0 +   40.0  
DP-0 connected primary 1600x1280+0+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
DP-1 disconnected (normal left inverted right x axis y axis)
HDMI-0 disconnected (normal left inverted right x axis y axis)
DP-2 disconnected (normal left inverted right x axis y axis)
DP-3 disconnected (normal left inverted right x axis y axis)

Though it changes the display size, both the screens had overlapping images. After so much analysis, I found one inconsistency in the output of xrandr, before and after scaling. Note the first two lines.

Screen 0: minimum 8 x 8, current 2560 x 1024, maximum 16384 x 16384
VGA-0 connected 1280x1024+1280+0 (normal left inverted right x axis y axis) 376mm x 301mm
...
Screen 0: minimum 8 x 8, current 2880 x 1280, maximum 16384 x 16384
VGA-0 connected 1600x1280+1280+0 (normal left inverted right x axis y axis) 376mm x 301mm

Individual screen's resolution has scaled to 1600x1280 from 1280x1024, but the total screen size is 2880 x 1280, also the screen's position is 1280x0 instead of 1600x0. So, to get over the overlapping problem, I used the following command, after reboot, and it worked

➜  ~  xrandr --output DP-0 --scale 1.25x1.25 --pos 0x0 --output VGA-0 --scale 1.25x1.25 --pos 1600x0
➜  ~  xrandr
Screen 0: minimum 8 x 8, current 3200 x 1280, maximum 16384 x 16384
VGA-0 connected 1600x1280+1600+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
LVDS-0 connected (normal left inverted right x axis y axis)
    1600x900       60.0 +   40.0  
DP-0 connected primary 1600x1280+0+0 (normal left inverted right x axis y axis) 376mm x 301mm
    1280x1024      60.0*+   75.0  
    1152x864       75.0  
    1024x768       75.0     60.0  
    800x600        75.0     60.3  
    640x480        75.0     59.9  
DP-1 disconnected (normal left inverted right x axis y axis)
HDMI-0 disconnected (normal left inverted right x axis y axis)
DP-2 disconnected (normal left inverted right x axis y axis)
DP-3 disconnected (normal left inverted right x axis y axis)

Now, you see that both the actual size of the screen and the starting position of the second screen is set properly.

Screen 0: minimum 8 x 8, current 3200 x 1280, maximum 16384 x 16384
VGA-0 connected 1600x1280+1600+0 (normal left inverted right x axis y axis) 376mm x 301mm
...