RecastNavMesh changes Agent Height back to 144

Agreed. I’m trying to shorten it to allow multiple NavMeshes (Floor + Hovering enemies)
It looks fine in editor:

But it just resets at runtime and only generates the top navmesh.
(Using instanced levels, so I can’t bake it)

Is there some way to change it through code at least? Atm I can only get the top floor working with dynamic navmesh generation.