fbx doesn't, is there an option to keep obj unmerged?

The merging may be due to all the faces having the same material. Houdini .OBJ output does not seem to forward the assigned material information into the exported .obj file format. The file format does support such features. You can re-write the .OBJ file, on export to add this functionality.

The code basically detects if the 'g' token exists. If it does, it inserts a new token 'usemtl' which many importers look for in breaking up the .OBJ.

There is a thread here, that discusses this.
https://forums.odforce.net/topic/25214-post-processing-an-export/?do=findComment&comment=146948 [forums.odforce.net]