What I think that they mean is that developing a completely new Silhouette Knight is long. Think about the time taken from the development of the war chariot to the tank (I know it is not the best analogy but it works), but developing small incremental updates is not so hard (think on different variants of the same tank model).
This is where Ernesti is making a revolution, each of his designs is completely new and he is creating a lot of new tech from the ground up.
Now let's tackle the commander units. The base soldier is given a standard SK but commanders are given slightly better units, maybe a hunt provided some better demon beasts so they have some custom ether reactors on hand, so they make a more powerful version of the same unit, and they can carry bigger versions of the same weapons. So basically they are the same unit but slightly better (think a barebones car, and a full-equip one, they are the same, but the full equip one, is more expensive and has better performance than the barebones one)