Why does Forest modify the material IDs of the geometry ?
In Forest, there is a big difference in comparison with the standard assignment of materials in 3DS. The material is NOT applied to the object, using the Material Editor, but selected as a parameter in the Geometry rollout, using the "Material" pick button.
Since Max handles Forest as a single object, it only can have an unique material assigned. In order to apply correctly all materials defined in the Geometry list, Forest collects all of them and creates internally a Multi-sub material, which is assigned to itself (named as "forest_automaterial"). This process is automatic and transparent to the user, but as side effect the Material IDs of the items don't match with the original geometry.
We use this approach for materials because is compatible with all render engines and Max modes.
Then, is there some way to use VRayMultiSubTex or other plugins based on Material ID ?
It is not recommended to use VRayMultiSubTex with Forest Pack due to the way the plugin redistributes IDs. If you must use it there are two options.
Firstly, you can disable Forest Pack's automaterial features by unchecking Consolidate materials. Be aware though that you will now need to manually create a single multi-sub object material, assign IDs manually and assign it directly to the Forest Pack object.
Alternativly, if the number total of items is not huge, use Forest Tools to create instances of the source objects. Since the IDs are not modified, you can apply VRayMultiSubTex without changes.