It does have implications. Since my v6 tunnel exits through the HE network, it may be advantageous to continue to recurse the Google queries through HE's DNS.
Google should be able to figure out that whenever they send a AAAA record to the DNS server on your IPv4 address, that they get an IPv6 query through HE.
I'll just have to try it both ways for a while each, and see if there is much difference.
One way to go about that is as follows. Run your DNS server without the forwarding for a week, and use it for your actual access to Google. Once per day try to do a AAAA lookup of the same Google domain using both your own resolver and the HE resolver. Ping each of the two IPs that you got to see which has the shortest roundtrip time.
If Google figured things out correctly, you should find that the IPv6 address you got using your own resolver gives a roundtrip time that is at least as fast as what you got using the HE resolver. If you got the exact same IPv6 address using both resolvers, then probably that is the optimal one, and Google managed to give a good reply to both DNS servers.