It is really dumb to force you sync every computer you've ever hook your iPod on! But it is not 100% stupid that it can only update that single song you put into the library. I've checked the speed and know it is just refreshing the whole library.
However, if I remove something from the PC library, iPod will not remove them during sync ...
If possible, use other stuff to transfer single file, like any sane people will do.