The black point is read from the dark pixels, a special area of the sensor that doesn’t catch light, and extracted by Rawspeed. You will find it in the raw black/white point module. Sometimes, it’s too aggressive.
You can fix that either in raw black/white point module or in exposure module, with the black level. Basically, you add some constant until your whole range gets positive.
However, the medium black threshold I’m talking about is not zero, but much higher. So even with no negative RGB in the pipeline, if you don’t have black point compensation on, you will still have black clipping on the print.