paul j3 added the comment:

One usage option is to make a subclass of HelpFormatter (the accepted way of 
customizing a formatter), and write a function that formats each group 
independently.  For the example case, the resulting format might be:

   usage: PROG [-h] [-b] [-a | -c] [-a | -d]

-h and -b are not part of any group.  These are followed by the two groups.  -a 
is repeated because it appears in both groups.

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<http://bugs.python.org/issue10984>
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