(What follows is somewhat speculative.)
Here is the quote from McGonagall:
"No, he's not dead," said McGonagall bitterly. "Unlike Dumbledore, he was still carrying a wand... and he seems to have learned a few tricks from his master."
While this could mean that a wand is necessary to sustain flight, I would argue that nothing McGonagall said precludes the possibility that she meant that a wand is necessary to take flight.
That is to say that to get from the ground to the airborne state of flying requires a wand (and whatever spell/magic is used to enable flight), but once the person is already flying, a wand (and whatever spell/magic is used to enable flight) is no longer necessary. You don't need to continuously perform the flying magic. You just perform the magic once to take flight and then you can continue flying without constantly renewing the magic.
I would argue that this is logical because if it is necessary to be continuously performing the flying magic, it would be a lot harder — if not impossible — to simultaneously perform other magic. Thus an airborne duel would be disastrous.
Moreover, we can draw somewhat of a parallel to broomsticks. Broomsticks are enchanted to fly when they are created, but we never find that a wizard must perform any magic to fly on a broomstick. Once the magic has given the ability of flight to the broomstick it can be flown without any continuous conscious performance of magic. Essentially, then, we can suggest that the magic that allows Voldemort and Snape to fly is in some way equivalent to the magic that allows broomsticks to fly. That is to say that the human being has been magically turned into a vessel of flight, and further magic is not necessary to keep it a vessel of flight.
Of course, one could then argue that one shouldn't need a wand at all to fly. The first time a person flies they would just magically enable themselves to fly, and then never need to specifically perform the flying magic again.
Perhaps this is even true in a sense. It is possible that the spell/magic eventually wears off, perhaps depending on the ability of the caster, so that one might be able to fly for a very long time without a wand but would eventually need a wand again to reinitiate the magic once it wears off.
So Snape and Dumbledore needed wands to fly because they were initiating the flight magic. Voldemort, at the moment he was wandless in the airborne battle was not initiating flight, but merely flying. Some prior point when he did have a wand was when he initiated the flight magic. Whether it was right before the battle (if it needs to be reinitiated before every flight) or whether it was at some earlier point (if the magic can last from flight to flight) he would have had the means to do so.
If this is true there is then no contradiction between McGonagalls statement and the facts of Voldemort's flight.
