To address your last point, about points not coming along - this is where Newton and RG3 are different. Why should we compare their point potential with past QBs, when they are very clearly different? The rushing TD from a QB record will be broken again this year, and the two will likely continue being threats for double digit TDs on the ground. That won't take away from what they can do through the air, enough to completely offset it. I have used this example before - say QBX also kicked field goals, and despite average passing stats, finished as QB3 because of his FGs. Would it be logical for us to suggest he can't improve on his numbers, because past QBs that didn't kick FGs couldn't?
You're overlooking a key point: Griffin and Newton don't kick field goals. They run. They aren't the only QBs in the league who run, and they aren't the only QBs in league history who ran. We have a long and rich history of running QBs to draw on. We have Cunninghams, and McNairs, and McNabbs, and Vicks, and Laynes, and Youngs (both Steve and Vince). We have a huge wealth of data on the career arcs of running QBs, and pretty much without exception, as they develop as passers, they regress as runners. Yes, both Newton and (likely) Griffin set the QB rushing TD record... But they were hardly the first to do so. Culpepper had 10 rushing TDs, and then never again topped 4. Mcnabb had 6 in 10 games, then never topped 3. If you think Newton and Griffin are unique, then you've already forgotten Randall Cunningham or even possibly a young Steve McNair.