There are 2 good reasons for this.
First, a TT bike is the most efficient machine for flat, fast course racing, where there are a minimum of hills. It is not the most efficient machine when it comes to climbing. The body position is far too aggressive for even professional athletes to use in a non-TT style event. A bike with more a more upright body position, a more stable weight distribution, a lighter frame, and far, far lighter wheels, is a more efficient choice for that style of ride.
Secondly, a TT bike sacrifices bike handling for that extreme power and aero efficiency. The TT stages are controlled events, where there are either one rider, or one team on the course at a time, and so limitations on stability and handling are acceptable. Take the same bike in a 150 rider peloton, where riders are constantly jockey for position, and where even on a stable bike losing focus for 1 second can cause a major crash, and all of a sudden, those same sacrifices in bike handling and stability are no longer a benefit for the rider or the team. They become a hazard to the team's chances of winning. And not just for the stage or the day, since a bad crash can take a rider out for the season. Or God forbid, permanently.
For these reasons, the UCI has seen fit to ban the bikes in non-TT events, in order to ensure rider safety. And for once, their decision makes sense.