Still testing quite a few changes and learning as I go... bear with me and after I get more info from the tests I will post about it.
You might try making a registry runonce call to a script. The script could contain a registry import of the desired options and perhaps copy files over old ones. There's more than one way to skin a cat, even if MS isn't playing ball with their xml settings
That's pretty much what I'm doing and testing now.. actually I using RunOnce and Active Setup which is getting most of what I want so far... I will report back as I make more progress