I'll try my best.
could you elborate on what you mean by a "standard level geometry system"
By a low-level, close-to-the-metal point of view, we only have drawcalls.
At an higher abstraction, those drawcalls come from various sources. They could come from a particle system or by meshes. There's a mesh which is way more important than others. The "world mesh" is typically larger, so large it needs intra-mesh culling, some sort of partitioning scheme. The system managing this "big mesh" is the "level geometry system".
Note nobody says this system must exist, it is indeed possible to use an assembly of generic meshes to make them appear to be contiguous. But I think having a "level geometry system" is still very valuable and I don't think it's going to go away soon.
For example, for Quake and Unreal engines the "level geometry system" is based on BSP-trees while generic meshes are not (but the BSP helps culling them AFAIK).
The whole point of the message was: instead of trying to turn a heightmap-based system into something that does not look like an heightmap, work on something more flexible.