Unfortunately there seems to be something going on with the AML kernel which intercepts certain keys and prevents them from been visible to the keymap editor, so some keys simply don't work. Its not a perfect vanilla transposition of the ir-keytable system as far as I can see.
I have not run in to this.
If a key is not remappable i would suspect these keys have not been defined through ir-keytable.
In this case it might be worth it to re-do the ir-keytable config and check if all codes are properly defined.
I have seen buttons on remotes that require a certain code to work in Kodi.
But then again, i am by no means an expert with configuring remotes; i keep it as simple as possible and/or have always been lucky