I agree that Incus shouldn’t make any assumptions, but I’m surprised that this isn’t configurable on Incus’s side. IPv6 router advertisements support the advertising of a prefix for address autoconfiguration without having clients register the router as a default route, and separately supports adding specific routes. I believe this could be done with dnsmasq command line arguments.
This is a question that was caused by my inability to make the solution here work, so maybe I can skirt the issue by only using one interface.