I am not sure regarding all vernacular. When I hear someone say such and such is a tool I see that as meaning the person will get the job done. Of course I am from a background as an automotive technician / mechanic / machinist so to me a tool has great value and worth. In that trade a tool can be priceless at times.
For example: "He is a good tool" to me would mean the person gets the job done and gets it done right.
Stack Exchange says its usage infers a person who is being used and does not know it. It also states, ""a stupid, useless or socially inept person" while further offers another inference of meaning being the penis. Reading all the input there it seems its slang infers many meanings. I would think context would be needed to know its true meaning.
In other words calling someone a 'tool' could be construed as calling someone a 'dick', e.g. "What a dick!" said as "What a tool!" Another view could be said as "He is just a dumb tool" offering meaning someone or something must direct or supervise the person in order for an objective to be accomplished. Or, the person is unable to think for them self.