Ghibli might be a more interesting case study - Miyazaki repeatedly said that he did not write his stories with an audience in mind besides himself, but his movies quite clearly have universal appeal. His stories are quite clearly grounded in his own culture, but they touch on universal human experiences.
However, there are definitely stories with a specific audience in mind that do not have universal appeal (e.g., Transformers smut fanfic) though generally authors are aware of this.
I think there are also folks who write stories with an idea in mind of universal appeal, but do not understand themselves enough to actually do so - things they take for granted as "common sense" may not actually be human universals. Or, because they fail to say anything at all in their work, it ends up fading into the background. (I don't believe in sociopolitically "neutral" works, we are all shaped by our beliefs and cultures).
These works aren't necessarily bad, either- I think Andy Weir has said a few times in interviews that his works aren't meant to be "political", but the two that I've read (The Martian, Project Hail Mary) are both a sort of "sci fi optimism" about people from different nations coming together to solve a problem. That may be "common sense" to some people, but it is certainly NOT a universal (even if I do share the outlook that people of Earth should work together to help each other regardless of national boundaries).
I think DS9 works if you consider it more as a "show about star trek" rather than just as "star trek". E.g., it's a good deconstruction of what is "necessary" for a utopia, or for looking at the limits of how a utopia van operate in practice.
DS9's characters and their dynamics are my favorite amongst any star trek show, but I think it's fair to say that the show does not stick to the core world building "pillars" of star trek. However, I think it would be unfair to dismiss it as simply edgy for the sake of edginess.
(Similar to KOTOR and star wars - really cool how the game turns the idea of the Force on its head, but definitely not in line with George Lucas' vision. I would still want to see a movie about this anyways)