Timeouts are definitely used as a functional tool according to my experience. They are used to mark a change of the strategic gameplan.
This typically happens (like in reality) when your team is behind and there is not much time left. Suddenly, your players do fouls on defense to save attack time (not necessarily, to the players with the lowest percentages from the line, but still...), start going more strongly for offensive rebounds, and throw more 3 pointers on attack (in relation with your tactics, yet regardless of the quality of your players' JR).
The result is either getting closer to the winning team by closing the gap (rarely I saw a turn over), or if your players sack at shooting from the 3 range - the gap will get larger.