Here's what a defender of the Amendment says about it:
The Federal Marriage Amendment introduced in Congress takes a prudent and reasonable approach to the problem. It abolishes same-sex marriage in the United States, and prohibits judges from legalizing other forms of same-sex unions, while preserving both federalism in family law and local self-government by protecting the authority of the legislatures to establish state policy regarding whether (and to what extent) to give some legal benefits to unmarried — including same-sex — couples.
Really, this is just another interpretation. Defender or not, I think it's being interpreted incorrectly.