Some characters (and even some player characters) will have the option to fly. In this case, scale works as expected, where abstract distances can be used to determine how close a character is. If the character is flying above the head of another, they are at best nearby.
Consider the size of a space to be the same horizontally as vertically when considering flying as it relates to movement. Therefore ascending or descending costs movement approximately as much as moving to adjacent spaces would.
While most flying capable characters will be using wings, while in danger allow for the pace of the situation to enable "hovering"; while not entirely accurate, this can be dismissed as swooping or circling, and removes the need for complex movement rules related to flight.