@Thanatomanic seems to have nailed it. If the objective is “to measure my camera signal to noise ratio”, then you want to look at raw values. No white balancing, no un-distorting, no demosaicing, no nothing.
Then the tool used (dcraw, darktable or Raw Therapee) should make no difference. The results should be identical.
If you include, say, a demosaicing step and the tools have identical demosicing then the results should also be identical. But you won’t be measuring the camera SNR.