As I understand it, there is no defined Z order for objects in the same drawing in 9-series products.
In Manifold 8, Z-order followed ID order, in reverse, so that the highest ID would always be drawn last.
This is not the case in SQL9, which is free to use multiple threads to fetch data and to draw data to screen. So although mfd_id looks like a linear series (often with gaps), series order is not available to control Z. So Z order in drawings is currently arbitrary in 9.
But if that is right, it is only one aspect of what you are seeing. Order is arbitrary, but why is only one point drawn? I would guess that the answer is Z culling, so that if there are multiple objects at the same location, only one object is drawn--the first or last object drawn hides any others--and that location is interpreted strictly, so that for points, formatted size is not material. Again just guessing.
So perhaps you will have to either use multiple drawings (whose relative Z order is defined), or use area objects. In the latter case not an overlapping stack of areas, but a set of rings, each net of the others, so that appearance is the same regardless of order. (Or almost--what about the border?)
Maybe this will change in future.