It's a starting point

It indicates that they were comparably thought of coming out of high school. (If you have a better/more accurate system for estimating the approximate ratings of two players at the same position, I'd love to hear it.)

Then Book got 5 years of coaching from Brian Kelly and company
Jones got 4 years of coaching from Nick Saban and company

I think that has almost everything to do with their respective performances on the field this year, who is the more complete QB, and who is the better NFL prospect.