Ooh, you caught an error I'd missed!
There's now a better ShipShape branch of the Python API to go with the new firmware if you're up for trying it: https://github.com/pimoroni/flotilla-python/tree/shipshape
The "Clear" result is the 4th, unfiltered sensor on the chip. It's 4 light sensors, 3 of which are filtered with red, green and blue filters. If you divide any of the other values by the "Clear" value then you get a relative-amount-of-colour-to-total-light, which is handy for getting relative colour values that don't change dramatically with the amount of ambient light.