I missed that $1000 part in the article. I saw the £200 more part (£550 in total for the board), which comes out at around $800 though, with a 700MHz G4. However this all depends on G4 pricing at the time (in 6 months time I imagine) and availablity, it could be cheaper, or it could be faster, or whatever.
But the trade-in offer is generous, but yes, "at current retail prices" doesn't mean "at purchase price", although it should mean a lot of good low-price G3-SE systems on the market early next year for a lot less money.