As with a lot of what I write, that is up to an individual GM to decide.
I would rule it to be situational - if the combat is occuring and part of the code of honour applies, then the bonus applies. For example, if one with a civilised or barbaric code has been seriously insulted, and the duel is to satify honour, I would allow it. Likewise, if one with a civilised/barbaric code is protecting someone weaker, then I would allow it. If one with a civilised code is attacking ordinary civilians who have not openly rebelled, then I would not allow it. Likewise, if someone with a barbaric code is trying to slay an honourable foe who has offered a ransom, then I would not allow it.
Of course, do what seems the most fun for you and your players. If a feat turns out to be not much fun, don't use it, or modify it until it becomes fun.