In Forest you can define multiple custom objects, each one using multi-subs and multiple IDs, so it's necessary to consolidate all of them in an unique sequence. This is the reason that Forest modifies the IDs in the resulting mesh, and create an auto multi-sub material which assigns to itself.
You can turn off Geometry->Consolidate Materials. In this case, Forest keeps the IDs of each object and doesn't create the multi-sub, but you are responsible to assign to Forest your own material.