With a 10 year old game, the rights of which may have changed hands a number of times since it was made, those files may no longer exist. In some cases, they may never have existed. And if the source code has disappeared along the way as well, then modifying the released game files somehow is the only way to do it. Whether that is done by the publisher or by GOG with the publisher's blessing, I don't know, and truth be told, don't really care either.
Frankly speaking, I would rather download the game from GOG all the while knowing that I won't have to worry about finding a torrent for the game, virus-scanning it, unraring it, and all the other hassles that are involved with torrents. Another positive is the better download speeds and the slight glimmer of hope that my (and other peoples') purchase sends a message to publishers to let them know that we would like more, instead of less, complex games.
Uhm, you DO know you're preaching to the preacher here, right? I wasn't criticizing GOG nor defending the RPGCodex loons ;-)