I created a line item validation per your recommendation - it works for the document type!
If a dedicated document type is used the system expects the cross-company code posting between the two company codes and checks if the G/L account is allowed (in the set). If the same Intercompany document type is used just to post in one company code (no cross-company), the system issues an error message too, which is fine.
Also, It tried to post via cross-company with another document type with and without the G/L account in the set - no error message is issued.
Now that the document type/G/L accounts are restricted, how do I make the users select the Intercompany document type or how do I restrict it? The main tcodes in use are FB50, F-02 and FB60?