Approach to upgrade application configuration
For all configuration settings that remain the same between configurations, have your installation script copy those over from the old config file if it exists. For the rest, just have some defaults that the user can change if necessary, as usual for a config file. Unless I've misunderstood the question, it sounds like you're making a bigger deal out of this than it needs to be.
By the way, you'd really only need one "updater" script, because you could parametrize the XML tagging such that it go through your new config file/config layout file, and then just check the tags in the old file against that and copy the data from the ones that are present in the new file. I haven't worked with XSD files before, so I don't know the specifics of working with them, but I don't think it should be that difficult.
My application has a xml based configuration. It has also a xsd file. Before my application starts, xmllint will check the configuration against the xsd file. 
With the growth of my application, the configuration structure has changed a bit. Now I have to face this problem: When I provide a new version of my application to customer, I have to upgrade the existing configuration. 
How to make this done easy and clever?
My idea is to build a configuration object using python, and then read configuration v1 from file and save it as v2. But if later the structure is changed again, I have to build another configuration object model.