Karabiner private swap modifier keys on a VM for real. No manual shortcut definitions no nothing else. How-to:

private.xml

<?xml version="1.0"?>
<root>
    <appdef>
        <appname>PARALLELS</appname>
        <equal>com.parallels.desktop.console</equal>
    </appdef>
   
    <item>
        <name>Swap Command and Option (Parallels)</name>
        <identifier>private.app_parallels_swap_command_and_option</identifier>
        <only>PARALLELS</only>
        <autogen>__KeyToKey__ KeyCode::OPTION_L, KeyCode::COMMAND_L</autogen>
        <autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::OPTION_L</autogen>
        <autogen>__KeyToKey__ KeyCode::OPTION_R, KeyCode::COMMAND_R</autogen>
        <autogen>__KeyToKey__ KeyCode::COMMAND_R, KeyCode::OPTION_R</autogen>
    </item>
</root>