Me thinks Fractal is a mathemagician (explains the name).
While it would "seem" that the offsets were random, and we use guesses to determine them, what if they were all corelated by some number like pi?
I don't believe this, but run with the idea for a minute:
Suppose the original text was written with the intentions of revealing its "secrets" as man became more aware of his surroundings. It would be easy to filter the text through a matrix and output an encoded document. It would be very difficult without the inverse matrix to return the original text. If (using pi as an example), we need to start on page 14, line 14 with the 14th digit of pi to output the original text, we would never know it. We might hit some numbers here and there, but until we knew the translation from one digit to the next, we would be poking around blind.
It seemed to me that the program explained positives too numerous to be artifacts. It sounded like the number of "hits" in the bible far exceeded the number of "hits" in Moby Dick. Of course all the typing shown was in Hebrew or something so I have no idea what they were really doing... not to mention that like Paige said, you'd need the first version of the book to prove anything.