The game uses the term "Manufacturing" in more than one sense. In the Harmony ideology tree, the first trait (I believe it's called Unification) gives a manufacturing bonus to the home world. However, this does not affect military production, only "social" production.
On the other hand, the Perfect Production trait (capstone to Creativity) gives 20% Manufacturing empire-wide, and this does affect military production as well.
I don't see any problem with these traits being the way they are, but it would be much less confusing if there were different terminology used to describe them. It should be clear from the description that Unification only affects Social Manufacturing.