If the internal flash is used as a Commander to control remote TTL flash(es), it HAS TO flash commands to the remote before the shutter opens. It is the Commander, it must Command (by flashing). It flashes commands (addressed to each enabled group), which are a request for a TTL preflash from each group. The remote (or remotes) answer in turn with a preflash, which the camera meters. Then the Commander has to flash a command to each group to program the power level for the final TTL flash (to each group, individually). Specifically, if you have two remotes, each is metered individually, and set to be equal at the subject (unless you have applied Compensation to one of them, for lighting ratio). So all this happens immediately after the shutter button is pressed, but before the mirror is raised. There is a lot of flashing, however it all looks like one flash to humans, we cannot distinguish them from the one final flash (except using Rear Curtain sync with a slow shutter speed can distinguish the time between them).
Then if the group for the built-in flash is enabled (in the commander menu), then the internal flash also will contribute to the flash exposure. But it can be disabled from contributing by setting its MODE to be "---" (in the commander menu). Even if the internal flash is disabled, the Commander must still flash commands before the shutter opens, but then the internal flash will not contribute. Except... after shutter opens, it still must then flash a low level trigger signal telling all the Remotes "OK, everybody flash, NOW".
That's what the commander does.
The commands are just low power ordinary regular flashes, containing both visible and infrared components (all flashes contain both). The remote flash units are red filtered to be sensitive to the infrared portion of the regular white flash.
So it is just semantics about the regular white flash containing infrared commands. However, the one SU-800 commander is filtered to only output infrared (does not make human eyes blink). See http://www.scantips.com/lights/awl.html for more, second page, but the $12 Nikon SG-3IR filter can be used on the internal flash, same purpose. The remote flashes will still preflash however.