You are correct in that speedo's are not that acurate, i use a GPS based Sat Nav that shows MPH and it shows a lower speed than the speedo by about 5MPH @ most speeds.
All top speed stats by the manufacturer will be based on flat road top speed.
Changing the sizes of your wheels will also alter the speedo reading, but not by much if you alter the tyre profile to match the increase in rim size, this still should fall within the manufacturers tolerances for the speedo.
By the way i have had my wifes MY02 TD4 manual up to an indicated 115MPH on a flat section of runway at which point i slowed down as it felt much quicker.
Zippy