The odometer/speedometer issue is actually very easy to explain.
With standard tyres on, the odometer is quite accurate (as you've observed). The ECU's calculation for speed is also quite accurate - ask your Scanguage for the ECU's speed, or ask Torque for its reading on it (it's in the list as "Speed (OBD)" which is just after the "Speed (GPS)" entry). You will find it remarkably close to the mark.
What's NOT accurate is the needle on the speedo that you look at. The figures in the ECU are right, the voltage sent to the needle is right, but the needle doesn't deflect properly for the voltage sent to it (that's the technical reason). Put simply, everything except that stinking needle is right!
That's why I keep advocating a GPS unit. If your tyres are out you'll need to cater for that difference in your fuel economy formula - a 5% variation (eg 255/70R16 to 265/75R16 tyres) makes a difference on a trip to Uluru and back.