The chosen phrasing is literally one step short of accusing the author of intent. "It could not have been designed better to [avoid detection] and cause harm" leaves open the possibility of accident, in the way that saying "this guillotine could not have been designed better to chop heads" leaves open the possibility of one spontaneously assembling from raw materials.
In my experience the phrase "it couldn't have been designed better to [negative thing]" is typically used, in a sarcastic, and usually exaggerated way, to mean "they did such a bad job, that they couldn't have done [negative thing] better, even if they had been intentionally trying to do [negative thing] (which they weren't)."