I agree, that's much more like the margin of difference. You can't compare a private ED 30 against a Dealer standard GTI - the comparisons have to be 'like for like' - otherwise it's meaningless. A dealer will have overheads, warranty, profit etc.....adding up to £2,000, at least, on exactly the same car.....opinion
Add in strong demand for ED 30; fewer in the supply chain, and there you have the £3000 difference.
The differences are significantly less than you seem to think. A quick search on AT, looking at 80-90k examples (around average miles for a car this age), shows the following:
Private...
http://www.autotrader.co.uk/classified/advert/201610028345968?search-target=usedcars&make=volkswagen&model=golf&year-from=2007&year-to=2007&minimum-mileage=from_80000_miles&maximum-mileage=up_to_90000_miles&fuel-type=petrol&minimum-badge-engine-size=2.0&maximum-badge-engine-size=2.0&page=1&sort=default&postcode=b902ee&searchcontext=default&radius=1501&onesearchad=new%2Cnearlynew%2Cused&logcode=p&adPos=3GTI, £5,995, 88k
Dealer...
http://www.autotrader.co.uk/classified/advert/201608307261150?search-target=usedcars&make=volkswagen&model=golf&year-from=2007&year-to=2007&minimum-mileage=from_80000_miles&maximum-mileage=up_to_90000_miles&fuel-type=petrol&minimum-badge-engine-size=2.0&maximum-badge-engine-size=2.0&sort=default&page=2&radius=1501&postcode=b902ee&searchcontext=default&onesearchad=new%2Cnearlynew%2Cused&logcode=p&adPos=1GTI, £6950, 85k
Dealer...
http://www.autotrader.co.uk/classified/advert/201609298244491?search-target=usedcars&make=volkswagen&model=golf&year-from=2007&year-to=2007&minimum-mileage=from_80000_miles&maximum-mileage=up_to_90000_miles&fuel-type=petrol&minimum-badge-engine-size=2.0&maximum-badge-engine-size=2.0&sort=default&page=2&radius=1501&postcode=b902ee&onesearchad=new%2Cnearlynew%2Cused&logcode=p&adPos=3ED30, £8995, 85k
Notice there is only 1k difference between the private and dealer GTI's. Certainly not £2k+ as you're suggesting.
Notice also there is only £2k difference between the dealer GTI and ED30? And the ED30 has DSG, Miltek, Revo, Stage 1 map, 18's, Kenwood Nav, Bodykit etc... I'm sure the mods aren't adding anything to the value here, but it does represent less money needing spent once you have bought it. I am unsure what a k04 conversion would cost second hand, but APR are more than the £2k difference here. I suspect after you take into account the extras on the ED30, you wouldn't have enough left over for a k04 conversion on the traders GTI.
I am also comparing vehicles here with good service histories, and recent cambelt servicing (DSG servicing on the ED30 too). There may well be differences in body condition, but that will only be evident upon viewing. For comparison purposes, they all look as clean and well cared for as each other.
Maybe, when you are looking at sub-40k example the difference there is more pronounced. But these are almost 10 year old cars now. There can't be many left with such low miles, so a premium for that should be expected, especially on limited edition models.
Basically, what I am saying here is, the cost differences between them aren't as much as you lot seem to think they are. My one was bought for £6125, with 97k, xenons, nav, H&R springs, Miltek, APR intake, Carbon Fibre Osir Engine Cover, parrot BT, full service history, just had it's timing chain done (belt needing done in April though) along with gaskets, tensioner, Cam follower, DV, etc, , brakes not long done, clean bodywork etc... I probably could have got a GTI with that spec for a little less, but it would only have been a little less.