You shouldn't need to modify /etc/resolv.conf. The plugin gets the DNS servers from the connection setup and puts them in /var/run/resolv.conf.gprs (which is where dnsmasq looks for them). I expect the problem with SIP and TOR to be the same as with MSN, having an IPv4 address embedded in the data. This means that DNS64 doesn't have a chance to rewrite the IPv4 address into a IPv6 one. So it probably won't be fixed without an update to that application.