I've not looked at the XML guts of VT for quite some time, so I'm not sure whether or not it's already supported. That said, it's commonplace to support some sort of "import" mechanism where custom settings can be imported to override the standard settings. It sounds like that's your aim.
I'd recommend taking a peek at ColdSpring 1.2's import mechanism, because it supports it. I also wrote an import mechanism for ColdBox 2.x. I have no idea if that's still out there available anywhere these days (that was years ago, and ColdBox is 3.5+ now).
HTH