The accurancy of capacitance measurement doesn't seem possible with this circuitry. Digital electronics occupy a large frequency spectrum. If this is a dedicated measurement microcontroller, what is the engineering addition difference.
You are right that there is too much noise when you measure changes of few fF but when using capacitive sensors capacitance change is usually 1pF or more and in this range it works very reliably so it is usable to get maybe.. 10 or 50 pF measuring resolution.
