In order to lessen influence of upgrade if possible, I am customizing lang and theme by below method.
Lang: I define phrase that I will change at qa-lang/custom folder(when use only one language).
Theme: I add new plugin for theme customization.
Note: Q2A core calls plugin after theme. Although it is not almighty, CSS and Layer of theme can be tuned by plugin. However, this method worsens Q2A performance a little.