The colors are real, mostly generated by thin-film interference depending on the thickness of the layers. Some people boost the saturation to make it more dramatic, but I think John's photos are natural.

There's a color chart here: http://www.htelabs.com/appnotes/sio2_color_chart_thermal_sil...

Mostly yes (ex: through thin film interference as mentioned), but there may be significant color correction for things like halogen light yellow color. There are also techniques to produce colorful images such as DIC and using a confocal microscope (ex: the 4004 ones I believe are confocal)