The boss may not always be right but he’s always the boss.
You are paid to do as you are told, not to question it. It is good that you try to do your best but if you are told to do something else then that is what you should do. You may not understand it, it could well be that it is mistaken to do that, but that is not the way any hierarchy works. If everyone decides how to best do their job regardless of what the boss said things would not work as well as if they do what the boss says, even if sometimes the boss is wrong.
I have been in both positions. When I am the boss I do not always tell every reason I have. I just expect my subordinate to do the best job of what I tell him, not what he thinks is best.
When I am subordinate I will definitely point out ways to improve performance but after I have had my say I will do as I am told.
This reminds me of a very similar thing. Some years ago I was visiting a friend who owns a restaurant on the beach. It was summer and the place was packed. My friend was very busy as was all the staff so, to pass the time, I started helpng out. I see a group is seated and I take them some menus. My friend says, here sit at the bar and have something to drink. But I keep helping. I see another group is seated and I immediately take them their menus as I see the staff is so busy. My friend finally (with some exasperation in his voice) asks me to not help. I can see it is not a good time to ask why so I just settle down…
I can’t help thinking why would you want to keep customers waiting for their menus? I didn’t get it but it was obvious he was doing it on purpose.
At a quiet moment a few days later he explained. The kitchen was too busy to keep up. If you give the customers the menu right away and they order, the wait time will be too long. If you make them wait for the menu, after they order they will wait less for their orders.
Well, even after it was explained to me I am not sure I understand it but here is the fact: my friend is the successful owner and manager of a restaurant and I am not. I have to assume he knows what he is doing. It works for him.
When I sail my boat I want crew who can efficiently carry out orders, not crew who know so much more than I do that they feel the need to discuss every move. By the same token, when I crew on another boat I keep very much in mind that I am crew and I am there to do efficiently as I am told. My job is not to teach the skipper what I may know that he doesn’t. This is not the time nor the place.
So, getting back to the OP, Rilchiam, you did the right thing by trying to be helpful and efficient, no question about that. But now the boss has told you to do it differently and he has his reasons which may not be apparent to you. They may be valid or they may not but you are not the boss to judge. It could well be that your boss is a moron and you are extremely bright and helpful but the world still works better overall if the boss makes the decisions and the subordinates abide by them.
Some day you might be the boss and you will appreciate this. 