I believe that what he is telling you is that, when you're missing a lot of GIR your putting should theoretically be really low because the shot that gets you on the green is likely a chip or bump'n'run or something and you should be getting it MUCH closer to the hole than you typically would from, say, 120-150 yards out. In that scenario you should be making a lot of one putts and when you do need to putt twice it's kind of equivalent to a three putt because you SHOULD have made the first putt.
Most people will find that the better they strike their irons the more putts they need simply because their first putts are typically farther away than if they had missed the green and had an opportunity to stick it relatively close with little chip shot or short pitch.
At least that has been my experience, the better I strike the ball the more my putting average inflates.
Or maybe he's just saying you suck, he can be a little grouchy.