Here's what's going on:

I elevated a cell and the combatant tried to move there but his pathfinding broke and he's stuck there. It doesn't matter if I do the cell elevation in the Scene view or apply an offset or set it up as a unique cell type in the Makinom editor, the result is the same.

In this example, I generated the grid on a relatively flat part of terrain, but you can see the corner cells are at an angle. I flattened the whole grid by selecting all cells and zeroing out the Y position and XYZ rotation, but this now causes pathfinding issues that weren't there before; it's like the mesh colliders from the grid prefabs haven't moved, and now combatants have trouble running into/over them.
One last thing I tried was setting up a new Battle Grid on a flat plane with a cube in the corner, so that some of the tiles would be generated at elevation. Even in this case Set Grid Cell Combatant actually set the combatant inside the cube, below the grid cells.