To document my final findings:
I wanted to tag regions that can be traversed by crouching and proning agents without using multiple graphs. To do this I added another job in “JobBuildTileMeshFromVoxels” called “JobFilterStanceSpans”, which does the same thing as “JobFilterLowHeightSpans” but instead of tagging unwalkable and walkable regions, it tags any span in the height ranges as tag 1,2, or 3 for stand, crouch, prone. This makes it so that the navmesh doesn’t automatically simplify these regions so that a GraphModifier that I wrote can tag these regions correctly.
This works perfectly except that I have to set the navmesh as the proning height, so the final correction so that I can set the navmesh agent height to their actual height is to change “JobBuildConnections” where voxelWalkableHeight is used and change that to the prone height so that regions smaller than the walkable height aren’t preemptively culled.