I just assume the AK was probably some Utopia where all races co-existed and not a homogeneous society.
I feel like it's likely DF's started taking form around the void century between the Gorosei not being named as ability users (indicating a possibility they're the original users of their abilities), and Vegapunk's explanation of how they came to be. I suspect that Devil Fruits emerge with a bit of irony, too. For instance, I could see Joy Boy just being some guy who wishes to be the most free person and bring smiles to everyone which causes them to give him a rubber body and boundless powers with respect to ridiculousness. IIRC Oda himself said he'd take Robin's fruit so he could draw Manga faster. I could see that being the explanation for that one. Some of the weirder ones like the Jacket fruit were definitely a product of irony.
In general I think Joy Boy started as a person and then became a symbol which is personified in the Nika fruit. That's to say I suspect as he gained fame stories about him took off and he probably gained some moniker due to his characteristics that became embodied in the ability he left behind which became a source of worship for those affected by him and passed down for generations.
I agree with this idea besides the idea they only took form around the Void Century for 1 reason. They must have always existed because they come from the desires of people. People would always have wished for freedom, to be invisible, to be tigers, etc.
I think Joyboy was just the first to Awaken Nika's DF since he was strong and wished to be free like Luffy.
On another note, I find it quite interesting that in chapter 1085, Imu didn't know Nefeltari Lili was actually a D. He only suspected this to be so because she betrayed them.
Makes me beg the question that how can someone secretly be a D. when the Ancient Kingdom was still present, and be a monarch, and no one knows?
If a Royal Family from France married a Spanish Royal Family member, one would assume their lineage would be common knowledge... You'd know the offspring isn't just French, but French with Spanish lineage.
Lili would have been probably an adult, she would have been well known, ruled for years, so why Imu is surprised at her being related to the Ancient Kingdom is odd.
Unless people can become D. simply by taking on the name and then keeping it secret, then it would explain why Saul was a D. as a giant, and it would also explain why Luffy was going to casually name Sabo as a D which seemed to be done in jest, but maybe it's just that simple.
OR, the D. people who leave the Ancient Kingdom tend to just keep their names secret, very interesting.
Perhaps, like you suggest,
they're a Utopia which would make sense.
Then I have to also question why haven't we seen a Mink or Fishman or other race also bare the D. initial? Is it we just haven't seen one yet, or they don't exist? Curious to say the least.