If you have something like IndexOptions FancyIndexing IndexOptions +SuppressDescription the second line is ignored. The reason seems to be that incremented_opts/decremented_opts are only added/removed to opts if the config is merged into another config. But the global server config is never merged into something else.
As a work-around, IndexOptions FancyIndexing IndexOptions SuppressDescription works. Though if the config is spread through many config files, it may be non-obvious that the lines are in the same context (global server config).