The valves under the black cover are there to operate the EGR valve. On your model, they do not operate the transmission. However, a leak in those valves can affect transmission operation, as the leak "robs" the transmission of needed vacuum. Unless you are concerned about having an EGR valve that operates, forget about the "black box." You are better off without it. It can't leak if it's not installed.

That being said, it is almost certain that someone will come forward with an anecdote about how they replaced their 3/2 valves or levers. And their transmission immediately started to shift smoothly. Therefore, they will conclude, the valves operate the transmission. But such is not the case.