And that's the argument, isn't it? How could 3/4 of a flagellum be of benefit to the organism?
The difference between simple and complex - lift up the hood of a modern car and look at the engine, life up the hood of a Model T and look at the engine. A Model T engine is vastly simpler but it still worked.
In biology, consider a cell membrane channel. Simple channels can be made of two proteins that can allow a molecule in or out of the cell. If any control is present, it is open or closed, movement is down the concentration gradient. A complex channel can be made of 8 or even 16 proteins with a myriad of subunit proteins attached. These channels can respond to cell potential differences, or receptor binding, or ion concentrations. They can even transport material against a concentration gradient. The have more flexibility and more control - same job.
A simple system does not mean parts are missing. It means fewer parts used to do the job. Sometimes it is not as efficient (modern cars are faster and have more power than a Model T) or doesn't have a high level of control (simple versus complex channels), but it does the same job.
Inter caecos, rex luscus
Inter caecos regnat strabus