The intake valves are used to control gas flow between the cylinder and the intake manifold. When the intake valve closes, it prevents gases from traveling in either direction. It's not necessarily true that inward flow would already have stopped, or that more flow would be desirable. The valve timing (intake and exhaust) is selected to strike a balance between efficient operation, power output, desired operating speed, etc.
Additionally, I don't think that throttling flow with a butterfly valve upstream of the intake has the same effect on pumping work that closing an intake valve earlier would have. Your previous statement seems to imply that you expect pumping losses to be the same (or similar) regardless of whether a butterfly valve is used, or early IVC. It does seem clear to me that using reduced lift (rather than reduced duration) to decrease air intake would have an effect similar to a standard throttle. To summarize, I think shorter intake duration is preferable to intake throttling, whether by intake valve or throttle valve, from the perspective of reducing pumping work.