It can't change the data though; that's just a load of proprietary format data that doesn't mean anything until it's converted into something meaningful. It's not even an image, it's just sensor values. Bibble might change some headers in it but can't bugger it up; you'll still, with any given settings, produce the same results again & again forever.
Edit to add: I use Adobe Camera RAW (CS2) and it generates those XMP files. It does also seem to 'modify' the .NEF (RAW) files but as I say, it can't be the sensor data.