From https://github.com/erasche/argparse2tool/blob/master/README.rst#limitations
Argument groups don't work in CWL as arguments are sorted with a special algorithm
According to https://docs.python.org/2/library/argparse.html#argument-groups argument groups are just presentational, they don't themselves dictate any particular sort order.
One could mimic the grouping by creating a http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputRecordSchema mapping the argparse title to the CWL label field (and eventually the argparse description to the CWL doc field)