You do not need to store function flags in web.config .
The option is to store them in a database - this has the added benefit of working efficiently in a web farm.
Note that with function flags, when you are in a position where the function will be either on or off (say, when switching from widgetA to widgetB, and you no longer need any widgetA code), you must remove the function and the associated flag. This will help in managing the feature set.
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