The pins/jumper you're referring to already serve a purpose; They tell the bootloader what to do.
In one position it simply loads the firmware which then presents itself as a HID device to the computer. This is what Simdash connects to.
In the other, the bootloader runs a different piece of software that provides an interface to write a new firmware image to memory, something that cannot be done while the chip is actually running.
In theory, provided those pins connect to a regular pin on the PIC, they can be repurposed.
Once the bootloader has checked their state, they serve little use. When the firmware is loaded, it could potentially use them for something else.
However, every time the device is plugged in, or the computer (re)started, it will require those pins to have a certain state to function properly.
This does beg the question, what sort of functionality do you see as an improvement to the product?
For clarity, I should state I am not a representative of Symprojects or Cristiano. I merely ask out of curiosity.