It's perfectly fair to compare Kobe Bryant's efficiency with LeBron James'. Both play similar positions (a SF should get some easier baskets), have similar roles (moreso when James was with the Cavs), and take a high-volume of shots. Thus if a formula wants to discount the value of scoring and increase the value of efficiency, to any arbitrary level, neither player is being that unfairly treated. This arbitrariness, however, becomes problematic when comparing players with different roles who take different shots.
On most possessions in the NBA, an offense cannot get an easy basket as the number of high-percentage shot opportunities (e.g. tip-ins, alley-oops, open ten-foot jumpers) is very limited against a professional defense. These opportunities are disproportionately given to low-volume scorers who are unguarded or close to the basket (see: Tyson Chandler).
Since the number of high-efficiency shots is limited, an offense needs players to take the medium- or high-difficulty shots. These shots are disproportionately taken by high-volume scorers (See: Jeremy Lin). Someone has to, for example, take a shot with the shot clock running out 25 feet from the basket while guarded by Shawn Marion.
The net result is that some players take very few shots and most of them are easy baskets while others take a lot of shots and most of them are not at all easy to make.
The same logic, to some degree, applies to turnovers.
. . . .
I can't touch on the statically methodology or the team adjustments.
. . . .
The player adjustments seem to reflect Berri's own biases. When a player meets or surpasses his expectation for what a player should be, he's rewarded. If he doesn't, he's punished.