It was probably used during development. Why bother with a JTAG port and some one-off development hardware or toolchain when Apple has already invested countless hours, engineers and dollars into its Xcode/iOS-based dev environment? This is even easier than debugging over Ethernet, which is what a lot of new set-top devices and current game consoles do. Recycling the dock connector even saves them having to come up with a new mechanical interface for the task.
Using Bluetooth in the remote would increase power consumption considerably - the CR2032 battery only has 10% the energy of the batteries in the Apple keyboard, for example, and it's non-rechargeable. Besides, any benefits of Bluetooth would be lost because consumers have been trained for decades to point remotes for line-of-sight operation anyway.
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