The question seems directed to me (appropriately so).
There certainly isn't any science to the "R" and "X" system (just like there isn't science to the star system either). I think it's impossible to "measure" most climbing dangers with much objectivity (it's kinda like trying to read the future).
Still, I do apply some criteria. Here are the major things I consider (leaving the actual definitions of "R" and "X" to what I already put in the book):
- Not over-using either rating (or else they become meaningless);
- Very, very rarely using either rating where the "dangerous" parts of the climb are more than two grades easier than the crux;
- Decades of experience climbing and decades of experience with Pinnacles specifically, applied with thought route by route;
- Overall perception of the route's danger (using the above);
- Concern for specific dangers (potential for a shorter fall onto a ledge might merit an "R" whereas a longer but "clean" fall might not);
- Thoughts about the quality of the route's protection.
Lastly, as to your question: "How would a new climber using the guidebook differentiate between easy 5th class old school routes with the same consequences as the new designated with a R?"
Theoretically there shouldn't be any difference between old and new, the above criteria should be applied regardless of the route's age. Realistically, if there is more of a tendency to give newer easy routes "danger" ratings it's because I climbed many, many of the older, easier routes before I kept careful notes, and, as one human being, it isn't as possible to field check every aspect of every route as I wish it was.
Finally, as an example, the above paragraph should make it clear why I was really, really eager to get J.C.'s field notes as I started to work on the new edition. He's made high quality notes to many, many of the "easier" routes that I simply don't have the time or energy to go back to. Honestly too, his views on these issues are - to my perception - quite parallel to my own and so I feel like I can heavily trust his comments (kinda like Munge's thoughts regarding fifth class ratings - I've always given great weight to Rob's fifth class ratings since they've always been very, very close to my own and, by definition, in my view, spot on).