If there had been a separate "--localconfdir" choice I would have been
    able to decide, on a per-package basis without having to patch it,
    whether or not I wanted it to live under /usr, or /etc, or wherever.

I think you are mixing two issues that ought to be separate.

1. Whether the program should make a special subdirectory to contain
   its config files.

2. Where the config files, or alternatively that subdirectory, should go.

I think it is fine if #1 is decided by the developer.  I don't think
it needs to be customizable.  Meanwhile, --sysconfdir specifies #2.

So the only question is, should we change the default for --sysconfdir?

I see the advantage of putting system configuration files in /etc.
The question is, is there any screw in doing so?

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