Most of the CPU pads can be muxed to work as GPIO, and most of them default to work as GPIO from reset. The JTAG pads, however, default to work as JTAG pads from reset:
The reason is that they need to work as such immediately if you want to be able to stop and debug the CPU before it runs any code.
To use them as GPIOs on youр device tree you must specifically change their IOMUX to work as GPIO. For example:
Anyway, in general, if you are going to use a pad as GPIO on your board, you’d better define a pinctrl where the pad is set to work as GPIO. Relying on the reset-default functionality of the pad is a bad idea because the boot loader might reconfigure a pad for a different functionality than the reset-default.