Timeouts are definitely used as a functional tool according to my experience. They are used to mark a change of the strategic gameplan.
You are right, but this only occurs at the end of the game as you mention as well. During early time-outs it's just talking without effect on the strategy(I assume?). What I stated above is what Steve Karenn mentions too. Maybe specific options for time outs could be implemented. Like choosing to stick to your original strategy while making fouls when behind in the fourth quarter or to opt for 3pt fgs and fouls. But maybe this should be in the suggestions forum:)