Ultimately this is a consistency issue. As noted, driving from one state to another could result in you becoming un-married (if only it was that simple ...) Civil unions are generally a state-level function, and the rules for marriage in California differ greatly from those in Virginia (ex. community property vs. dower law.) All would be well and good should you never cross the state border, but when you do, does the adjacent state recognize your civil union? Married in one state, but living in another - which estate rules apply? Further, the Fed has stuck it's fingers into the pie, and chooses to recognize the civil union through the IRS. That *should* create a situation where consistency flows top-down, but as there is no Federal courthouse from which you may seek a marriage license (at least, none that I'm aware of,) the process must flow up-then-down.
I expect the Fed wants to push a "Consistency in Marriage Act" onto the states, where "any two people age 16 or older may join in a civil union." I just don't think they have the authority to do so. The Fed *could* just treat people as individuals, and leave the civil-union business to the States. However, that would erode their power base, which makes me think it's unlikely they would even consider doing so. My gut says they will do something emotional, pandering to the married masses, and make things much worse overall.