You'd have to configure your displays as separate X screens, not a shared desktop. Ubuntu should then let you adjust the sub-pixel order for individual X screens.
Otherwise, what would happen with a window that spans two display devices with differing sub-pixel orders? Or even trickier, two displays in clone mode with different physical orders (RGB vs BGR).
This is a known limitation for all the operating systems right now and would need a major redesign to get it fixed. Dynamic adjustment isn't feasible because the library doing the rendering would have to know which screen you are on and adjust dynamically. Plus, suppose you have half of a window on one screen and half on another - it wouldn't know which to choose.
Setting up multiple X screens:
- Boot up and reconfigure X.
sudo dpkg-reconfigure -phigh xserver-xorgFollow the steps to set up the primary display. (I don't know of a way to do this particular step from CLI)
- Open up a terminal and
 lspci
 This should give you a list of your devices and their bus ids. Find the graphics card and write down their bus id's.
- Make a copy of your xorg.confasxorg.conf.origmaybe and open it:sudo vi /etc/X11/xorg.conf
- Read this BEFORE proceeding to make sure you can customize it as much as you want.
- Now make two - Devicesections and list the- BusIDof the card to be shared and also list the driver like this:
 - Section "Device"
    Identifier  "nvidia0"
    # Your preferred driver
    Driver      "nvidia"
    # Edit the BusID with the location of your graphics card
    BusID       "PCI:2:0:0"
    Screen      0
EndSection
Section "Device"
    Identifier  "nvidia1"
    # Your preferred driver
    Driver      "nvidia"
    # Edit the BusID with the location of your graphics card
    BusId       "PCI:2:0:0"
    Screen      1
EndSection
 
- Now create two - Screensections (with the parameters of your choice of course, the only thing that needs to match is the- Devicein this section to the- Identifierin previous one) as:
 - Section "Screen"
    Identifier  "Screen0"
    Device      "nvidia0"
    Monitor     "Monitor0"
    DefaultDepth 24
    Subsection "Display"
        Depth       24
        Modes       "1600x1200" "1024x768" "800x600" "640x480" 
    EndSubsection
EndSection
Section "Screen"
    Identifier  "Screen1"
    Device      "nvidia1"
    Monitor     "Monitor1"
    DefaultDepth 24
    Subsection "Display"
        Depth       24
        Modes       "1600x1200" "1024x768" "800x600" "640x480" 
    EndSubsection
EndSection
 
- Now make a - Monitorsection for each monitor as:
 - Section "Monitor"
    Identifier "monitor name here"
EndSection
Section "Monitor"
    Identifier "monitor name here"
    # Rotate as you want (your question says one is rotated)
    Rotate "left"
EndSection
 
- Finally, update the - ServerLayoutsection to use and position both- Screensections:
 - Section "ServerLayout"
    ...
    Screen         0 "Screen0" 
    Screen         1 "Screen1" leftOf "Screen0"
    ...
EndSection
 
- Restart X and cross your fingers! If it does work then go on fine tuning it as much as you like. 
NOW FOR THE SUBPIXEL RENDERING ORDER
Do this change in font.conf either in ~/font.conf or /etc/X11/font.conf`.
      bgr 
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