In my opinion you better have different hole for the gen set. The diameters of exhaust pipes are generally only sufficient for which engine they are designed for. You cannot use two systems at the same time.
Another drawback might be mixture of exhaust gases and water from one system to the other. Although the exhaust sysystems are non return pressure of the gases might force them to return to the other system. When you are running the gen the gases and water might be forced to the engine and vice versa.