My take is that Moon Knight can't fly. However, *Khonshu* can make him fly, by his own power and intervention ( at least at night ). This requires Khonshu to actually choose to use MK as a channel for such an effect, though, which is dependent on how much Khonshu actually feels like acting in his own right. Remember, Khonshu is a dick.
Basically, there are powers Moon Knight has as a benefit of being an avatar, which are dependent on the costume but ultimately under his own control ( as long as Khonshu doesn't strip him off his avatar status or get imprisoned, natch ). This would include enhanced physical stats, healing, various weapons and armor that are controllable by his thoughts, and the ability to perceive and interact with mystic forces. Then there are things Khonshu can do, which Moon Knight as avatar has the privilege of asking be done, and even if done are *not* under his direct control.