This API query returns the aliases of various SE sites. For MathOverflow (with main domain mathoverflow.net) it returns
"aliases": [ "http://mathoverflow.stackexchange.com", "http://mathoverflow.org", "http://mathoverflow.com" ],
But the second one, http://mathoverflow.org, does not function as an alias for the Q&A site; rather, it's a blog of MathOverflow, Inc.
(This came up in relation to Why do some Stack Exchange sites have their own domain names?)