I haven't thought of the particular point you bring up. CVS could be of help here if you've set things up with the future in mind.
For Greenpeace we set up a scheme where individual national organizations can provide their own templates to be used instead of the default templates. This means, among other things, that there's really no reason to edit the templates that come with the toolkit - a custom version can be made instead.
The way this is done isn't generalized though, being quite tied down to the organization of the site.
But it's caused be to think that something vaguely like this might be interesting to try to develop for acs-subsite instances. If we remember that "/" is just the top-level subsite a scheme that allowed for the substitution of standard templates with subsite-specific templates would perhaps be useful. At GP we made the substitution possible on the level of a single default template (just .adp not .tcl files as that fit the need). The kind of tracking you're discussing also applies to .tcl scripts ...
