Yes, the stat benefits people who go to the line a lot and make their FTs, as well as good 3pt shooters. That is especially true for Manu, who is the designated FT shooter for many of the technical fouls and end-of-game situations, because the other starters suck at free throw shooting.
Many stats people prefer to use adjusted points per shot, which adds FTAs to your number of shots acc. to the approximation 1FTA~=0.44FGA. For instance, basketball-reference.com calculates this adjusted points per shot for all players over a season.
Manu's regular season adjPPS was 1.22, very good. His playoffs adjPPS was an awesome 1.30, but I am not sure if that is the best ever for a perimeter player.
It doesn't look unprecedented. Brent Barry, for instance, averaged 1.336 adjPPS over an entire season in 2004 with the Sonics (now where is THAT Brent????), so maybe someone else got past 1.3 in the playoffs. Someone can go do the research.
Whatcha gonna do when Huxamania runs wild on you?!!