Romney would have won under the Congressional District method

[Vosem]

Democrats also won the nationwide popular vote for the House of Representatives.  Voters wanted the Democrats this election, and instead they get another Republican majority in the House.

^^^^^^^
They need to make this a key talking point. Even stupid people can understand why this is Inksed up. It would also further erode Boehner's legitimacy at a time when he is already facing an avalanche of trouble on all sides.

Are one-party general elections and unopposed races taken into account for this?

Not only are they not, if you take them into account you likely get a Republican victory: http://www.dailykos.com/story/2012/11/08/1159272/-Dissecting-the-House-Popular-Vote