Not the heights, but the former individuals sitting in the chairs.
It's based on both, really.
We know where each member sat based on cutscenes, but for pictures like that of YMX, there's no context where you can tell where they are sitting (for instance, if we could see where the Nobody symbol on the floor was aligned, we would know for sure because it points to Xemnas' seat), so you have to base it on the heights of the chairs in relation to each other.
And checking the heights of the chairs is accurate.
The chairs can move, but the fact of the matter is that they don't. Only time we have ever seen them move is during the competitive multiplayer on Days lol. Other than that, in all cutscenes, they have always been at fixed heights. Xemnas' seat is always the highest, Xaldin's the second highest, Xigbar's the third, etc. And this still bears true in KH3D, we can see from other scenes (eg the one at the end of the Special Trailer which gives a nice view of the seats) that they are all in the same positions. Really, there'd be no reason for the developers to adjust the heights of the seats anyway.