Most everything that customizes the hardware is outside that directory. For example, rc.local for setting 444, tweaking of the remote via lircd, and anything dealing with OS-level file sharing.
Some remotes just have a bad lirc config. Mine had two different buttons mapped to the exact same lirc key.
The PITA was that they weren’t even close to the same function…one was “Previous Chapter”, and the other was “Back”. I can’t recall what they were both mapped to, but one way would be that every time I tried to skip back a chapter, the movie was put into the background and I was navigating the movie list, and the other would be not being able to back out of menus.
The op that asked the question in the other thread was referring specifically to his Kodi config. I’m quite aware that this would have no bearing on other OS customizations or package configuration.