NA-TT are also harder to value IMHO, things such as service history from the previous engine, history of the transplanted engine, servicing and maintainable since the conversion should all be recorded or factored in when valuing the car.
I genuinely don't believe in the years to follow that converted cars will continue to command the same price as non converted cars, although they won't be lagging too far behind with the correct paper work, and perhaps diff upgrade etc.
I sold a TT-Auto recently, it was owned by myself for the last decade and the mileage was genuinely low and documented throughout. I sold it for £8k+ and was satisfied with the sale as I held out for a genuinely enthusiastic buyer.
I guess the situation of a seller comes into pricing also, I was in no real rush (although the wife will say different) and managed to get the price I wanted. I realise that this is not always the case with other sales, so prices can vary great due to this factor.