I'm not sure that the line check figure was deliberately set high on the BT checker, otherwise <insert name of regulator / competitor / minister here> would have come down on them like a ton of bricks for misleading the public etc.
This is pure speculation, but it may have been based on distance from the exchange and some coefficient to cater for going round the houses a bit. Unfortunately this probably couldn't take into account the way-longer-than-average routes that some lines take.
I also think that the checker does take into account the figure stored for lines to neighbouring properties, and it routinely seems to adjust itself based on neighbours. Perhaps the results are adjusted based on calculated / actual connect rates grouped by postcode area or property?
Not sure what happens with new lines now, but when I moved in here in 2004, the BT checker said 500kbps, red for 1Mb, since it was a new number. I managed after some pushing to get that raised up to 1Mb, and then 2Mb, and I'm now syncing at ~10Mb on ADSL2!
Whilst I was on BT max, I managed to sync at 8Mb pretty much all the time, yet the BT checker said 5.5Mb.
BT are their own worst enemies by not publicising enough information about how their network and planning works, and so what we "know" is really a collaboration of what people have deduced. However, whilst I'm certainly not questioning your findings, I'm unconvinced that false greens are a deliberate act by BT - they are more hassle for them after all. And surely there are enough conspiracy theories in the world already