"Many clients have multiple partners like GS or PI or VN in a PO"
to be honest, I have never seen that, and would not even know how to make it possible, which is actually the question here. Since you are saying it is quite normal then you probably know how to make it possible.
I hope you are not mixing contracts here. whenever a vendor or a contract has a several partners for the same role, then a pop-up is issued to have the user select just 1 entry.
Especially different VNs do not make any sense, one PO cannot have several vendors.
ME359 cannot be made a warning message, it is hardcoded error.