I'm personally on the side of those who prefer clean configuration files, and a proper documentation on the nature of the configuration file which provides all necessary information about things possibly missing in the file which is actually used.

So, since you already have tools which check the dependencies, you could generate a hyperlinked documentation of those sections and their contained items, which could be checked just in case and, in the productive configuration files, just one line of comment for each missing section, according to the config files convention, containing a link to the missing section's documentation.

That way the "just in case" folks have their reference, and the others would see the clutter as having been drastically reduced.