[Toucan]

But when driving a manual car the driver doesn't put the clutch in while braking until almost completely stopped.

If you need to slow down quickly enough that you're not just letting the car coast in the gear you were driving in then using the brakes to bleed some speed off isn't going to be less fuel efficient than down-shifting to a gear that will stop you in time. The engine is engaged for almost exactly the same period of time.