Yeah, the order in which players actually get drafted will change somewhat in every franchise. We're simply recording the projected round that the game lists for the players. Since we can't know how teams will actually draft when the situation in each franchise is different, that's all we can realistically do.
This helps people using the guide to know whether they have a shot at a particular player or not. If my team holds R1 Pick 7, then I can't bank on getting a Top 5 projected player. He may end up falling to pick 7, but there's no way to know that, and it will change between franchises.
Also, this was, by far, the most asked question from users of my 2011 guide, but in regards to online franchise. Online franchise works completely different, since there are no projected rounds and everyone can see all the stats of the players (except for potential) before the draft. For online franchise, the guide really isn't very helpful other than to show Potential ratings (A, B, C, etc.) These guides are mainly useful for Offline.
-rdm