No worries - I thought it was likely "me" as no-one else was reporting similar. When you mentioned the github changed I saw the VERSION piece and it clicked then.
Portainer is just being a smidge too clever 
It's recreate holds everything that is set, including BY the container (running config). I've taken those VARs out of the compose file now and set it as a Portainer stack, so I can still recreate the container (on it's own) OR restart the stack, which should pull the whole lot.
I'm moving my DNS to a stack anyway as I've got a custom DNS front end Container which does some mobile/roaming security AND runs a DNSCrypt connection, feeds into the pihole container, and then piHole is pointed back to the DNSCrypt connection. (sounds messy, but it works).