Yes, but accelerating the entire train is going to cost way more energy than accelerating the transfer car. Also, the transfer car can simply use wheels and brakes to gain kinetic energy from the train, so it can be incredibly light. Even if a longer track and motor are necessary for high speed bullet trains, there would still be a big energy savings.

Also, no matter how quickly you can accelerate to make a stop quickly, the same train will be able to save considerable trip time with the transfer car system. Saving a half hour or hour off of trip time from a route is certainly worthwhile, especially if it means that the train can run the same route at a lower top speed. The energy savings from that could be enormous over the long term.