The TilemapRenderer generally works on the XY plane and has a flat XY bounding box in 3D space. The TilemapRenderer can be culled from 3D lights if there is a large Z difference from the light itself.
Setting a Transform matrix for a set of Tiles does not automatically increase the bounding box for the TilemapRenderer. To help with that, you can make use of the "detectChunkCullingBounds " and "chunkCullingBounds" properties of the TilemapRenderer. You can set the "detectChunkCullingBounds" property to Manual and increase the Z value for the "chunkCullingBounds". This will prevent the 3D lights from culling the TilemapRenderer when rendering the lights.