Golden State is just so well put together as a roster. That is what a roster in today's NBA should look like. A point guard/leader who can stretch the floor while creating in the PnR game (who's secure in his position w/little ego), 2 wing players who are elite shooters, a 4th starter who's a junk yard dog and does the dirty work (the 5th guy is just there to set up quality lineups when they start to sub), along with a veteran PG off the bench (Livingston) who's very solid/efficient, and Igoudala is another junk yard dog off the bench.
Houston is too guard oriented with very little production in the 3-5 positions. The lack of talent there is the reason for this, not the system. Harden controls so much of the ball, it renders Chris Paul ineffective a lot of the time. Eric Gordon is a solid player, but at 6'3 is a little short to play the 3. Houston had Patrick Beverly and traded him away for Paul (desperation to keep up with Golden State). If they had him, they'd be better. They are also missing Trevor Ariza. If Houston could get a guy like him (Jaylen Brown @Boston), they'd be right there with Golden State.
As far as the call, James Harden gets by with this all season long and nobody says anything because it happens on a Wednesday night at midnight in February. When the playoffs kick in, things get tighter, etc. he still looks for the same BS and doesn't get it. Very similar to how Peyton Manning always complained about physicality with his receivers in the playoffs. Sorry, man, you're not going to get the same calls in playoff action.