It is not safe to modify directly the automaterial, because Forest keeps internally references to the materials, that would create unexpected results if they are modified externally.
I suggest to modify directly the materials of the Geometry List (they are accesible in the "matlist" property). Any change on them, will be updated safely in the automaterial. In this case, would be necessary to create a "Blend" for each material, but this process may be automatized by Maxscript.
Regarding the XRef question, i think you can xref the objects but not the materials.