Take the following with a grain of salt in that it’s probably outdated, but it may also be something to consider if you’re not planning on using capes:
A few year’s back on BBB, we ran across an issue where config-pin gave an error when attempting to reconfigure pins that were already in use by the cape manager/cape universal. At the time, I THINK, there was a way to disable the cape manager/cape universal via changing a variable/flag setting in uEnv.txt. I think that was on an image around the time the transition to U-boot overlays was going on…
The following post shows a line in uEnv.txt for enabling, and I assuming disabling cape universal:
So, not sure if this means that if you change to 0 in uEnv.txt, that it would free up pins so that pin-config no longer gives an error.