My guess as to why:

Two reasons.

First, I doubt if they sold enough manuals to warrant the costs involved in developing and certifying the emissions to make it profitable.

Second, I expect emissions certification is a lot more difficult with the manual. With the automatic they can simply program out conditions that result in excessive emissions.

Remember, too, the manual D-max is derated compared to the automatic, so there must also be some durabuility issues.