This is what they do, but it negatively impacts the game. Plays don't develop properly, and it closes off a lot of openings that would normally exist for the offense. On the other end, it makes it very difficult to play good defense when the CPU can sit in the paint for a quarter of the shot clock. It's been one of my biggest issues with the game for a while.
Quick example: Ilyasova gets the ball in the paint, with me guarding him. He sits in the paint for 5 and a half seconds before passing the ball back out and leaving, with no call. I've given up a lot of points this way because I play it like the call will come after three seconds.
I didn't do it this time, but oftentimes I will jump for a block after about 2 and a half seconds, anticipating the shot to avoid the 3 second call, only to have them dribble around me for an open layup using those extra three seconds.