Phone chargers already convey more than just electricity. Any 'smart charger' or similar will include some data exchange through the cable, so that the charger can actively change its voltage rates in a way that the phone's battery and programming can take advantage of.

The construction of a cable has enough room for a small chip to interact with what it plugs in to. If Apple wants to make their cords proprietary and not just the charger, then they can include a small chip that adds a small amount of data to the interaction. Then the programming of the phone can change how it takes advantage of the charger based on the existence (or lack) of this extra data.

A similar practice happens with ink and toner cartridges. Off brand cartridges can be rejected by a printer's programming, even though the only difference are the chips and wiring that interacts with the printer to tell it "on brand cartridge" or not.