Hi,
See https://sourceforge.net/p/ptpd/mailman/message/32775661/ and following.
This is a set of patches to be applied to the trunk in version r248. This enabled UDP over IPv6-Transport.
We have been using it internally for the last two years.
I have limited personal knowledge of the reasoning behind the changes but will try to answer any question that comes up.
Regards,
Philipp