I agree that DJ is just an average putter by tour standards and also agree that strokes gained putting is the most correlated putting statistic with someone's actual putting abilities. With that said, I don't think SGP is perfect- it only accounts for distance and not the difficulty of the putts you have. Not every 3 foot, 7 foot, or 27 foot putt is created equal. Some players do a better job leaving themselves easier putts.
My take-away with Spieth is that the stats seem to confirm he is an intelligent player with no weaknesses- while he is only 40th in GIR, he is 7th in strokes gained with approach shots. This tells me he is either getting it closer than most when he does hit a green and/or, when he does "miss," it is in the right spot more than his competitors. Being on the fringe is technically a missed green, but it is a likely a good shot if you are only 15 feet away from 175 yards..