Does this mean that every Pinephone is also constantly running this secret proprietary non-updateable machine?
It's possible to just not load the modem firmware and have Pinephone as a device with two ARM SoCs both running mainline Linux and open bootloader. ;)
You'll just not be able to use EG25-G as a modem with modem FW not loaded. There are also options in between.
Pinephone may have a phone in name, but it's basically a neat little SBC with an integrated touchscreen and battery, and bunch of other peripherals, and can be used for anything you like.