the use of the jig does not, but the act of flashing/hacking does void the warranty.
rightfully speaking, all kinda hacking/flashing activities voids the warranty, as it tempering the phone from the manufacturer's intended/allowable usage.

the USB jig can be used to reset the "custom rom flash count" superficially to "0" / "No", when pairing with the right bootloader version, giving "better impression" when you try to RMA.
the more important use of the USB Jig is to allow you to go into Download mode, when phone is semi-brick and all other methods failed.

if you check the LYN i9100 thread, it seems that Samsung is not so particular in denying user from RMA claim just because the user has flashed a custom rom / kernel before.