So CCD's are true 16 bit and CMOS sensors are 14 bit up sampled?
I've just done a photo test of Phocus vs Lightroom on Hasselblad Files, as well as Canon to Hasselblad files, there does appear to be a slight difference in Colour definition between my Canon and Hasselblad files. With the Hasselblad appearing to have slightly more colours in them. Well to me anyhow.
Phocus_Vs_Lightroom
Canon has lagged behind in raw sensor image quality and still do if we consider the noise aspect. Today with the 5Ds they're lagging behind less, but still a fair bit behind the latest Sony sensors. That's why so many are using say the A7rII with adapters on Canon glass. In other words Canon is not a great role model if you want to see what the best CMOS can do today.
With CCDs the sampling is not on the chip, but outside and there 16 bit analog-to-digital converters (ADC) have been used. With lots of noise. Some formats have stored the noise (like Hassy 3FR) some has not (like Phase One IIQ). With CMOS the ADC sits directly on chip (lower noise), and nowadays they're 14 bit with incredibly low noise, so no they're not "upsampled".
Comparing colors are tricky as what you see is more the effect of the profile and color filters on the sensor than anything else. Although noise have some effect, all fairly recent sensors have low enough noise to not be a significant factor concerning color in well-exposed areas.