The Commander mode setting for the built-in flash will send a series of pulse trains but if the mode is set to "--" no flash will contribute to the exposure. The only problem I have seen is the pre-trigger light pulses can trigger someone's blink reflex. CLS is a complicated system that requires the camera and all the slaves on each channel to communicate with each other by sending and receiving pulse position coded data by flash. Pressing the shutter release causes the camera to send out a pulse of light telling all the flashes on Channel A to fire a reference level of light output which is then metered by the camera, and the sequence repeats for each channel. The camera calculates the total light reflected back from the subject. The camera sends a code by pulse code to each channel separately in sequence that tells each channel how much power to generate. The camera then send a code to fire all the slaves. It the build-in flash is set to TTL while in Commander mode, its power calculation has already been done by the prior measurement command sequence since the camera was able to measure the reflected light from the built in flash every time it was used as the code transmitter. The built-in flash has its power set at the same time, after applying the flash compensation value stored in TTL mode. If the mode is changed from TTL to "--", all the flash sequence is performed by the built-in flash except for the very last one....the one that is fired during the shutter being open. You can try an experiment to prove that. Remove the external flash but keep the camera flash in Commander mode and set it to "--" and take a photo in a dark room. Black frame even though you see all the pre-flashes, which are so fast that they all appear as one short flash. Change the mode to TTL and dial in flash compensation of your choice (I use it as direct flash as -2-3ev just to get a little catch light) and take a photo of the dark room and you will see an image under exposed by the amount of the flash compensation bias you dialed in.
If you really do not want the flash to go off, the alternative to optical coding is wireless RF flash triggers. Fairly recently manufacturers of wireless triggers have started relaying the coded information so they can be used in a CLS setup. I designed my own CLS compatible RF flash triggers 4 years ago for my D90 and I did not even know at the time, it was not possible with any commercial product. I never bothered to build it into my D7000 or D800 however. Stan St Petersburg Russia