As we can read in this thread  dnsmasq doesn't permit to specify a custom
mtu for ipv6, this is needed on out setup to avoid batman-adv level
fragmentation, so the actual solution in dnsmasq doesn't work because it
requires to put a lower mtu on specified interface and we cannot ( and don't
want to do this )
Gui can you ask to dnsmasq developer to add this option so dnsmasq can work
good also on our setup ?
P.S. With al we have debuged some mtu iussue and committed fixes