Well if done correctly that should be the only thing used when doing a boot.ini change. Just have to make sure to save the original and then the modified under different names. I have done this thousands of times. I know XP is better at hidding the boot.ini but it isnt that hard to find with all files showing. If you can find it them something must of went wrong somewhere with the edit to not have done it right.
Well that is a way to view it. It does save it but i dont think that over rides the default. Doing the edit boot.ini is the way i have known for years. That was the only way to do it back with 95. That was the only reason i suggested that.