Peter Eckersley added the comment:

Thanks for your feedback Paul! I agree your proposed implementation strategy 
would probably be saner; I'll revise the patch to use that approach or 
something like it.

As for the question of necessity, there are definitely more cases than just the 
store_false ones -- I documented these in the linked Certbot bug but very 
briefly they include:

* Programs where the default value of a variable is "Ask interactively" if no 
flag is provided
* Cases where the default value is the result of some complicated computation 
(for instance, reading it from a defaults file)

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<http://bugs.python.org/issue28742>
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