The generally accepted cause of hangovers is drinking too much. Fusel alcohols can cause headaches but for me, the causes of my rare hangovers are 1) too much to drink, 2) dehydration, and 3) too little or bad quality sleep.
Id say also when you choose to clock off on the beer helps too. Say you just have an afternoon session but finish at dinner time i feel pretty good the next morning. But if i carry on right up to bed i can feel pretty average the next morning .
For people in general I think the answer has to be both. Some people will react to ingredients coming from different processes (though I suppose that's technically not a hangover) while for others it's down to their ability to process the alcohol.