Another way to play with the defaults is to use argparse.SUPPRESS.  With such a default, the argument does not appear in the namespace, unless provided by the user.

In [2]: p = argparse.ArgumentParser()
   ...: p.add_argument('--foo', default=argparse.SUPPRESS, help='foo help')
   ...: p.add_argument('--bar', default='default')
   ...: p.add_argument('--baz');
In [3]: args = p.parse_args([])
In [4]: args
Out[4]: Namespace(bar='default', baz=None)

Such a namespace can be used to update an existing dict (such as from a config file), changing only keys provided by user (and ones where SUPPRESS does not make sense, such as store_true and positionals).

In [5]: adict = {'foo':'xxx', 'bar':'yyy', 'baz':'zzz'}
In [6]: adict.update(vars(args))
In [7]: adict
Out[7]: {'foo': 'xxx', 'bar': 'default', 'baz': None}

User provided value:

In [8]: args = p.parse_args(['--foo','foo','--baz','baz'])
In [9]: args
Out[9]: Namespace(bar='default', baz='baz', foo='foo')

In this code sample I used Ipython.  That IDE uses (or at least did some years ago) a custom integration of config and argparse.  System default config file(s) set a large number of parameters.  Users are encouraged to write their own profile configs (using provided templates).  On starting a session, the config is loaded, and used to populate a parser, with arguments, helps and defaults.  Thus values are set or reset upto 3 times - default, profile and commandline.

I for example, usually start an ipython session with an alias

alias inumpy3='ipython3 --pylab qt --nosep --term-title --InteractiveShellApp.pylab_import_all=False --TerminalInteractiveShell.xmode=Plain'

Regarding this bug/issue, if someone can come up with a clever tweak that satisfies Thermi, is potentially useful to others, and is clearly backward compatible, great.  

But if this issue requires a less-than-ideal-compatible patch, or greater integration of config and argparse, then it needs to be developed as a separate project and tested on PyPi. Also search PyPi; someone may have already done the work.