It has nothing to do both "separate but equal" if the only difference is the legal term used ("marriage" for heterosexual couple, "civil union" for homosexual couple) and not the rights associated with it.

Separate but equal was about physical segregation of minorities, not just about using different legal terms for the same thing. And, by the way, something that a ton of people don't know about the separate but equal doctrine (because it doesn't appear to be taught in American public schools): It actually refers to the government's legal authority to mandate that privately owned businesses provide separate nut equal facilities for blacks. That's a lot different than the usual portrayal of Brown vs. BoE, as the government stepping in an conquering private racism.