I believe best current operational practice for DNS over IPv6 is to send only 1280 byte UDP frames.
Then again, I don't think it is completely agreed upon how to get past the 512 byte limit that DNS was designed with.
The DNS request is unlikely to go past 512 bytes in the first place (it is actually not that easy to construct a valid DNS request larger than 512 bytes). The reply can easily be larger than 512 bytes, and it used to be the case, that you were supposed to switch to TCP in that case.
The client can include an EDNS option specifying that it is capable of receiving larger packets, and then the server can send a reply larger than 512 bytes, and larger than 1280 bytes even. But some consider this a problem because it could be used in amplification attacks.
With all the things that need to go on to ensure that DNS packets larger than 512 bytes are permitted, you'd think that PMTU discovery could be completed by the time you are ready to send a large packet. Unfortunately PMTU discovery is a bit less efficient than I'd like it to be. Why do you have to waste bandwidth sending a maximum sized packet to find the MTU. Potentially you'll need to send multiple large packets before you find the actual MTU.
I think a better option would have been a hop by hop option that contain the MTU seen so far, and is then decremented by each router along the path if it cannot handle as large a packet as indicated by that option. Then you'd just need a small packet going back and forth to find the PMTU. Unfortunately introducing such an option now is of limited value, because it would have to be supported by most routers in order to really help.