The transmitter (SU800) and the pop up flash do exactly the same thing - Emit a infrared pulse that triggers all the flashes. For the pop-up to do this, it must fire its normal flash as well (the flash releases both frequincies... you just can't see the IR. Camera filters can see all the wavelengths that our eyes can't. To keep them from messing things up, manufacturers put IR filters over the sensors to remove the light before it hits the sensor.
Your pop-up triggers the remotes with a pre-flash. It will only contribute to the exposure (which happens after the pre flash) if you have it set to fire a second time (adjust the master flash to -- in your CLS menu). Sometimes you can catch a reflection of the preflash in your shot, but otherwise the effect is negligible.
The limitation with both the Nikon transmitter (which is really just an IR flash) and the pop-up, is that they are using high frequencies that travel only a short distance and can't penetrate solid objects. If you move down the spectrum to radio waves, then you get lower energy, further traveling waves that can move through things like walls, light mods, and over sized lighting assistants. This is why you get radio in your closet, but you don't get sun-light). Radio is a better solution for long distance transmission, but its also harder to choreograph in such a way that you can calculate things like TTL exposure. That's why most radio poppers restrict you to manual control only.