So, basically if you craft mk II armor you get new bonuses.
If you have f.e. Superior Metal Armor with some bonuses and craft from it Metal Armor MK. II you basically get only it's condition but new set of bonuses (if you are lucky).
When you upgrade weapons bonuses stay as they were without changing it's stats.
I would rather change it to the point of armors. It should give some life to lower guns with bonuses from crafting and give more way to obtain upgraded weapons from those which don't have bonuses. What do you think guys?