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Darks are taken to deal with hot pixels, not to deal with noise.
Noise is averaged out later in stacking process.
That is why it appears there is more noise if you use darks AND internal long exposure compensation - that means darks were subtracted two times from frames, and that defies the purpose of taking darks.
Now, when to take them, that depends.. I have the feature enabled (400D) and I have no problems.. (it only takes 2x longer to actually take images, but then again, I am not in a hurry.. and this way I know the darks were taken at the same temperature as frames.
It is good idea to take flats with the same procedure (with darks).. for the sake of consistency of the whole process.
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