Ninety-seven chapters in and I yet do not understand why Witch Hat Atelier (WHA) is marked seinen. Despite its tragic themes, it does not have the grittiness of Vinland Saga or Berserk. Demon Slayer and Attack on Titan have arguably more darkness than WHA, yet they are labeled as shounen. Also with the number of teenagers in central positions, the manga deliberately circumvents adult themes and emphasizes simplicity, cuteness, and all that you would expect in shounen or shoujo.
As far as I can tell, the reason why Demon Slayer and WHA do not belong to the same genre is that Coco is a female lead. The shoujo genre clearly does not apply despite the female lead.
Witch Hat Atelier is simply a dark shounen with comedic elements and a teenage female protagonist. Perhaps a different genre label needs to be coined. Seinen simply does not convey the right idea.