The fact is, Cryptic puts features in the game, and then ignores them. If they work, then great. If they don't work, which is usually the case, no more resources are devoted to actually fixing them. Fixing bugs seem to be given absolutely no priority.
The scaling is another feature that was hastily added, and ignored. It doesn't work. It only works if you not only scale but also use a low level ship and equipment (which defeats the entire convenience). Even then you'll do a little too much damage, but it won't be as outrageous as if you use your normal ship and weapons.