Given that he's actually charged more for postage than a 3kg prepaid satchel with eBay's 10% cut added, I wouldn't be overly impressed either, not when he's clearly paid the standard 500g rate. Hitting him with a low postage DSR isn't going to do him any damage or cause him a defect so there's no real point in doing that.

I think I'd be emailing him and suggesting that he must have made a mistake with postage as he's clearly charged over double the cost of a 3kg satchel instead of the correct 500g rate, and ask him what he intends doing about it. No need to mention feedback as the implication is fairly obvious.

If he apologises and refunds most of the overcharge, I'd give him positive feedback but if his attitude is somewhat defensive, I'd very seriously consider a neutral, and if he becomes aggressive or ignores you completely, I'd have no hesitation in negging him. Of course, that's just me; your opinion may differ slightly.

P.S. I can't stand postage pirates so my reaction may be somewhat harsher than yours.