You're right, Orion wouldn't be a very good vehicle for a crew for the entire voyage. And TB eloquently explains that the final view of the mission hasn't been determined.

There will be other modules, including one or more for habitation. And NASA, sadly, is soliciting other countries for assistance with this project. Much like ISS.

(Given the size of the US budget, the priorities of the US budget, it's a crying shame NASA doesn't get more.)

And it's not surprising that the re-entry module looks like Apollo. Given the mission and the parameters there may only one good solution. Soyuz looks to be about the same, too. Until newer materials come along we may be lucky we have even one way to get it done.