First of all, there's a difference between "RetroArch" and "RetroPlayer", the first being a standalone project, and the second is the code name for a "player core" in kodi that plays games. I assume you mean the second? RetroArch is a separate process and thus wouldn't support any controller configuration from within Kodi.
Second, can you upload a debug log that shows you playing a game and pressing a button that doesn't work? I only see 14 lines in the log you posted. Given that Kodi's controller system is so massive, a debug log will give me a sense of where in the system your presses are getting dropped.