This leads to 2 errors, one irritating, one that prevents the program from functioning.
Irritating: GTK+ loads the system GTK theme during a call to gtk_init(). If this theme is based on clearlooks but contains declarations unknown to our (older) version of Clearlooks, you get errors.
Blocking: GTK+ loads the system GTK theme during a call to gtk_init(). If the theme file defines a "color theme", then when Ardour defines its own, GTK will block for ever, because of a bug in GTK+2. This doesn't happen if the system GTK theme has no color theme definition.
Those are the two main issues. They cannot be worked around without rebuilding the GTK+ stack so that it cannot or will not load the system GTK theme.
If you've contacted GTK about upstreaming your patches, what was their response? I'd be surprised if they didn't want to.