At an altitude of 100km, Spaceship One was not held aloft through lift via the atmosphere.
Actually, it was. Spaceship One did not achieve Earth Orbit.
you misunderstand. Spaceship One achieved freefall. After rocketing into space, or as you put it the upper atmosphere, the wings no longer supply lift to the vehicle, and it enters a projectile motion, going up at first but steadily accelerating downwards (during this period the pilot experiences weightlessness) until it reenters denser parts of the atmosphere, and the wings supply lift again.
In fact, Spaceship One's trajectory was more or less straight up and down. Not very conducive for generating lift, even in the denser atmosphere.
Spaceship One is an airplane with wings. It generated lift through the atmosphere. It is not possible to generate lift in a vacuum. Therefore Spaceship did not go into space, even if it came extremely close to it.
See: Jeep-Boat analogy
Yes it generated lift through the atmosphere, but after it rocketed into space, it followed a freefall trajectory which brought it back down into the atmosphere, where the wings then provided lift once again. The process is referred to a sub-orbital spaceflight. There is no intention in the flight to "stay aloft" while in space.