... seems to be completely undocumented.

Getopt::Long's documentation does document it, though not directly (emphasis added):

The call to GetOptions() parses the command line arguments that are present in "@ARGV" and sets the option variable to the value "1" if the option did occur on the command line. Otherwise, the option variable is not touched.

It's just a little leap from that that you can take advantage of having an option's variable set before its passed to GetOptions, which is what the odd code given does.