About 3. Yeah the tribal tattoos apply effects so they are being tracked, their effect definition is just empty and they don't get referenced anywhere either so it's a bug.
About 4. Since the cour_set function clearly caps the courage to a maximum of your grade limit or less if reduced by traits i think it clearly is a bug and it is located in the traits section where multiple traits ( devoted, slutty, pretty voice, scarred, dominant and submissive ) apply their values straight to the variable rather than going through the proper helper functions.