A related issue, not mentioned on this list so far:
I'm v6-multi-homed at home with
2a00:1030:100::/48 2a00:1030:1004:1000::/56
and RA-announce two prefixes/gateways on the probe's net. It's a matter of luck whether the probe auto-configures its primary address to the prefix I'd prefer (the one also used in the static prescription). (That's not specific to the ATLAS probe -- a lot of my gear is non-deterministic in this respect.)
At my home I have 4 IPv6 prefixes (2 from xs4all, HE, and 6to4). The best way to retain some sort of sanity is to make sure that all but one are deprecated.
Alternatively, make sure that all just work and that it doesn't matter which one is used. The main problem there is reverse DNS.
my home is also IPv6 multi-homed. I expect the RIPE probe to probe using both source addresses. my routing infrastructure does SADR, so the probe by choosing source address also chooses exit. cheers, Ole