What does "tool" really mean?

According to Green's Dictionary of Slang, tool has several meanings. In the current context it would probably mean "a stupid, useless or socially inept person". The first citation for this dates from 1656.

I suspect that this meaning is derived from the first meaning under the headword "tool", "the penis", as a literal or figurative bodily organ (first citation 1553), as names for the reproductive organs are frequently employed as terms of abuse (can't think why).

The meaning of "unskilful workman" appears a little later, at 1698.

In the first paragraph of the link you're referring to, he explains exactly what he means by "tool":

I just offered a bounty on one of my questions and selected "Draw attention to question" as the reason since it is the only one that applies; the question had low views and no answers (or votes). However, the description that is shown makes me sound like a pompous idiot.

And later in the post,

That way I could have specified that I just wanted a solution without looking like I'm infatuated with myself.

Whatever the general, common, definition is for "tool", there's no better clarification than two descriptions in the same source text.

From Urban Dictionary:

1. tool
One who lacks the mental capacity to know he is being used. A fool. A cretin. Characterized by low intelligence and/or self-steem.
That tool dosen't even know she's just using him.

It does depend a bit upon context.

Hugo's answer is certainly one possibility, but another is a derogatory epithet derived from the OED's meaning 2b: "A bodily organ; spec. the male generative organ (or pl. organs). Now slang."