If you use the camera's inbuilt flash in commander mode it doesn't have any noticeable effect on exposure unless the subject is very close to the flash. What is of more concern doing it this way is that the burst of light that commander mode gives could still have a fogging effect if there is a lot of moisture in the air.
I initially experimented with using the wireless TTL (commander mode) underground. I used a separate commander unit (more on that below) rather than the inbuilt flash but found that the strobe had to be within sight of the camera to fire which was pretty useless for most of the lighting setups I wanted to try. Hence I shifted to using a firefly with the flash in manual mode.
To set off the firefly I used the popup flash in the camera (I have a D70s) with an infrared filter. The filter I use is not a crappy bit of film over the flash but instead attaches to the hot shoe. It came with the nikon close up flash kit which is a really excellent bit of kit if you like closeup photograhy. The close up kit comes with a commander unit (SU800) that only fires infrared (no visible light) which eliminates the fraction of a second delay you'll notice you get in commander mode but as mentioned above isn't very good underground. The infrared filter, on the other hand works a treat. Not sure if you can buy them separately but I expect an email to Nikon would find out. Nikon describe it as SG-31R IR Panel for Built-In Flash.
I put the inbuilt flash into manual mode when using this. It then fires one burst rather than the multiple flashes you get in commander mode before the main flash, which means you can get away with using a firefly 2 rather than the more expensive firefly 3.
Have fun playing with it and post some pictures