You can always add a custom field to the master data to differentiate materials (or use company code which is there by standard if I remember correctly).
The vendors have this information by default anyway once they are "true vendors", therefore in replicated status (on the integration tab).
For the business documents, only those groups will have visibility who are on the document as collaborators anyway, so I wouldn't worry about that. (you can also default those on the templates if you would be worried about having to add a bunch of people all the time).
As for the document, yes, it can still only flow to the respective back-end system if PI is provided with the right logic (for example, the material data quoting the right company code -> provided that is only relevant for one of the systems).
Bests,
Niki