With the new atmospheric model, how long is an average ship expected to be able to hover in place before the thrusters overheat, versus ships with dedicated VTOL engines?

Okay. So I'm not going to say how long. The VTOL engines will be more efficient in that, because a good chunk of the main thrust is being used to hover. So VTOL-capable ships will be able to hover longer before the engines overheat. But in general, the engines of all ships will not overheat fast. You will always have enough time to land. Otherwise, it would be pretty frustrating.