USB-C actually has pins dedicated to application/debug use (SBU1 and SBU2). "SBU1 and SBU2: these are low-speed lines used only for Alternate Mode and accessory mode. For example, with DisplayPort, AUX+ and AUX– transmit over the SBU lines. For audio adapter accessory mode, these lines are used for the microphone input and analog GND."

As long as it's not intended for user to plug in, it's fine. Many other vendors also do that.

Mining rigs were using USB-C to transport PCIe x1 by the truckload. Because USB 3.0 cables are dirt cheap and are capable of transporting signals at PCIe x1 data rates.

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Cost. It's a clever hardware hack that saves money, and 1 cent saved over 100 million units is $1,000,000!