How would I remap Mac CMD to CTRL keys in Blender?
Your private.xml is missing the only key and would swap the keys system-wide. Additionally you got the naming of the item wrong.

Here is a working private.xml:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
    &lt;item&gt;
        &lt;name&gt;Enable at only Blender - custom&lt;/name&gt;
            &lt;item&gt;
                &lt;name&gt;Swap Command and Control&lt;/name&gt;
                &lt;identifier&gt;private.swap_command_and_control&lt;/identifier&gt;
                &lt;only&gt;BLENDER&lt;/only&gt;
                &lt;autogen&gt;__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L&lt;/autogen&gt;
                &lt;autogen&gt;__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L&lt;/autogen&gt;
            &lt;/item&gt;
    &lt;/item&gt;
&lt;/root&gt;


or if you want the "For applications" to appear in the private section:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;
    &lt;item&gt;
        &lt;name&gt;For Applications&lt;/name&gt;
        &lt;item&gt;
        &lt;name&gt;Enable at only Blender - custom&lt;/name&gt;
            &lt;item&gt;
                &lt;name&gt;Swap Command and Control&lt;/name&gt;
                &lt;identifier&gt;private.swap_command_and_control&lt;/identifier&gt;
                &lt;only&gt;BLENDER&lt;/only&gt;
                &lt;autogen&gt;__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L&lt;/autogen&gt;
                &lt;autogen&gt;__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L&lt;/autogen&gt;
            &lt;/item&gt;
        &lt;/item&gt;
    &lt;/item&gt;
&lt;/root&gt;




If you want the key mod to appear in the non-private part "For applications" you have to add it (the most inner item key including &lt;item&gt; and &lt;/item&gt;) to the file: /Applications/Karabiner.app/Contents/Resources/include/checkbox/apps/blender.xml. 

Any Karabiner update/upgrade will remove/overwrite your mod probably.

Example:

&lt;?xml version="1.0"?&gt;
&lt;root&gt;

  &lt;item&gt;
    &lt;name&gt;Enable at only Blender&lt;/name&gt;

    &lt;item&gt;
      &lt;name&gt;FlipScrollWheel&lt;/name&gt;
      &lt;item&gt;
        &lt;name&gt;Flip Horizontal and Vertical ScrollWheel at Blender&lt;/name&gt;
        &lt;identifier&gt;remap.app_Blender_flipscrollwheel&lt;/identifier&gt;
        &lt;only&gt;BLENDER&lt;/only&gt;
        &lt;autogen&gt;
          __FlipScrollWheel__
          Option::FLIPSCROLLWHEEL_HORIZONTAL,
          Option::FLIPSCROLLWHEEL_VERTICAL,
        &lt;/autogen&gt;
      &lt;/item&gt;
      &lt;item&gt;
        &lt;name&gt;Flip Horizontal ScrollWheel at Blender&lt;/name&gt;
        &lt;identifier&gt;remap.app_Blender_flipscrollwheel_horizontal&lt;/identifier&gt;
        &lt;only&gt;BLENDER&lt;/only&gt;
        &lt;autogen&gt;
          __FlipScrollWheel__
          Option::FLIPSCROLLWHEEL_HORIZONTAL,
        &lt;/autogen&gt;
      &lt;/item&gt;
      &lt;item&gt;
        &lt;name&gt;Flip Vertical ScrollWheel at Blender&lt;/name&gt;
        &lt;identifier&gt;remap.app_Blender_flipscrollwheel_vertical&lt;/identifier&gt;
        &lt;only&gt;BLENDER&lt;/only&gt;
        &lt;autogen&gt;
          __FlipScrollWheel__
          Option::FLIPSCROLLWHEEL_VERTICAL,
        &lt;/autogen&gt;
      &lt;/item&gt;
    &lt;/item&gt;
    &lt;item&gt;
      &lt;name&gt;Keys&lt;/name&gt;
      &lt;item&gt;
        &lt;name&gt;Swap Command and Control at Blender&lt;/name&gt;
        &lt;identifier&gt;private.swap_command_and_control&lt;/identifier&gt;
        &lt;only&gt;BLENDER&lt;/only&gt;
        &lt;autogen&gt;__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L&lt;/autogen&gt;
        &lt;autogen&gt;__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L&lt;/autogen&gt;
      &lt;/item&gt;

    &lt;/item&gt;

  &lt;/item&gt;

&lt;/root&gt;


with the result: