1. This so-called worker cannot pasul the company’s matzos on a whim. The mere fact (?) that he asked for a raise proves he’s an extorter and nothing more. I would kick him out the door on the spot. If someone needs support for this position, read some of the Chasam Sofer’s tshuvos on shochtim.
2. When and if he operated the machine, the end product was more than one box. He could not possibly remove lishmah from only one box , numbered or not. This is an automatic process, with hundreds if not thousands coming out after a few buttons are pushed.
3. In my opinion, the mere process of baking shmurah matzah automtically confers lishmah on it. Hundreds or thousands of years ago, the baking process was an everyday fact of life and the matzos needed to be singled out for Pesach. Nowadays, it is obvious what these matzos are for, and so they are lishmah automatically.You can disagree, but my opinion is perfectly logical.
4. I am aware that many gedolim do or did not not approve of machine matzos, especially the great Rav Chaim Tzanser. To each his own, no problem.