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:
<?xml version="1.0"?>
<root>
<item>
<name>Enable at only Blender - custom</name>
<item>
<name>Swap Command and Control</name>
<identifier>private.swap_command_and_control</identifier>
<only>BLENDER</only>
<autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
<autogen>__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
</item>
</item>
</root>
or if you want the "For applications" to appear in the private section:
<?xml version="1.0"?>
<root>
<item>
<name>For Applications</name>
<item>
<name>Enable at only Blender - custom</name>
<item>
<name>Swap Command and Control</name>
<identifier>private.swap_command_and_control</identifier>
<only>BLENDER</only>
<autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
<autogen>__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
</item>
</item>
</item>
</root>
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 <item>
and </item>
) to the file: /Applications/Karabiner.app/Contents/Resources/include/checkbox/apps/blender.xml.
Any Karabiner update/upgrade will remove/overwrite your mod probably.
Example:
<?xml version="1.0"?>
<root>
<item>
<name>Enable at only Blender</name>
<item>
<name>FlipScrollWheel</name>
<item>
<name>Flip Horizontal and Vertical ScrollWheel at Blender</name>
<identifier>remap.app_Blender_flipscrollwheel</identifier>
<only>BLENDER</only>
<autogen>
__FlipScrollWheel__
Option::FLIPSCROLLWHEEL_HORIZONTAL,
Option::FLIPSCROLLWHEEL_VERTICAL,
</autogen>
</item>
<item>
<name>Flip Horizontal ScrollWheel at Blender</name>
<identifier>remap.app_Blender_flipscrollwheel_horizontal</identifier>
<only>BLENDER</only>
<autogen>
__FlipScrollWheel__
Option::FLIPSCROLLWHEEL_HORIZONTAL,
</autogen>
</item>
<item>
<name>Flip Vertical ScrollWheel at Blender</name>
<identifier>remap.app_Blender_flipscrollwheel_vertical</identifier>
<only>BLENDER</only>
<autogen>
__FlipScrollWheel__
Option::FLIPSCROLLWHEEL_VERTICAL,
</autogen>
</item>
</item>
<item>
<name>Keys</name>
<item>
<name>Swap Command and Control at Blender</name>
<identifier>private.swap_command_and_control</identifier>
<only>BLENDER</only>
<autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::CONTROL_L</autogen>
<autogen>__KeyToKey__ KeyCode::CONTROL_L, KeyCode::COMMAND_L</autogen>
</item>
</item>
</item>
</root>
with the result: