You are correct, the APQ8016 can do more things with the GPIOs than the minimal required functionality as defined by the 96Boards specification. The provided software doesn’t take advantage of the additional capabilities, but you can rebuild the kernel and take advantage of the hardware capabilities of the APQ8016. The risk to taking advantage of the capabilities of the APQ8016 is anything you do will most likely not be supported by other SOCs. As long as you are locking your code/product to APQ8016 then go ahead, but if you want forward compatibility with future SOCs, then care should be taken.
Full disclosure, I am an employee of Qualcomm Canada, any opinions I have expressed in this or any other post may not reflect the opinions of my employer.