I think your over emphasis on shots at the rim is missing the larger picture. For one it could be a deliberate decision of the strucure of the offense by the coaches as much as it is inherent differences in the PGs games.
Another point is that Rondo takes 2 less 3s and 3 less free throws per game than Rondo. That easily accounts for the much of the at the rim difference.
But that's not a bad thing, CP3 is a much more efficient scorer and diverse scoring threat because he can get to the line (and make them at a high percentage) and also hit threes.
I don't know why a coach would want to emphasize jump shots over shots at the rim, but I suppose anything's possible. And a large amount of CP3's free throws aren't from shooting fouls.
The top ten teams at generating shots at the rim
1. Denver
2. Toronto
3. Memphis
4. Charlotte
5. LA Clippers
6. Chicago
7. Detroit
8. Utah Jazz
9. GS Warriors
10. Boston
I guess there are 9 point guards better than Rondo with the likes of Mike COnley, Chsuncey Billups, Rodney Stuckey, Jerryd Bayless etc...
Also, if you look at shots 3-9 feet (where you can factor in Paul's deadly floater) Paul is in the top ten in makes and attempts while Rondo isnt in the top 30 in either.
Also, if you look at assists of baskets less than ten feet, Paul is in the top 6 while Rondo is 22nd.
Dunks and layups arent the only high percentage shots.
By the way, Dallas was next to last in shots attempted at the rim...