Any pins listed as GPIO can be reprogrammed. PINMUX software (perhaps in combination with the device tree firmware file) can be used to add or remove binding to a function for those pins. For example, the J21 pin 13 is listed as an audio-related function, but is provided through a pin the TRM lists as GPIO_PE6 (Linux kernel naming gpio38)…this means you could disable the audio part of this and use it instead for your own GPIO purpose.
However, I imagine to control a drone you must have a wire somewhere unless you are wanting to use a wireless receiver between the Jetson and the drone. Wireless would be ordinary network programming, but I imagine using one of the serial UART interfaces, I2C, or GPIO would be easier (serial ports are fairly common use and easy to work with). You do not necessarily have to use the pins of J21, there are other connectors available with either UART or GPIO. A real answer would require more details on exactly which part of drone control you are interested in…lots of people do this, I’m sure someone would have suggestions if there were more details available on what you want to accomplish.
Also know that the developer carrier board is not the only way to mount the JTX1 module. There are several third-party carrier boards available, some of which provide a lot of I/O beyond what the developer carrier board provides.