Here is a theory I came up with after watching a YouTube video covering the possibility that each Devil Fruit has its own soul. That theory is based on the idea that Devil Fruits have the souls of devils in them, which is why you cannot eat two Devil Fruits because the souls of the devils will fight with each other. This theory goes on to explain that the souls of the Devil Fruits influence the person who eats the DF, ex. Big Mom wasn’t super devious until she ate the Aoul Fruit. This could also explain the link between JoyBoy and why the Gomu Gomu no Mi is such an important fruit.
So, if you believe that DF’s have inherited will’s, you start to wonder where the original will comes from, who first imprinted their will on the DF? We know that DF’s popped up during the Void Century. We also know that during the Void Century, there was a giant war between a superpower country and 20 other countries which later became the World Government. So, what if the thing that sparked the war was the superpower country inventing Devil Fruits? What if they developed a way to create these Devil Fruits by imprinting the will’s of certain strong warriors into them? This new technological development would have made this country unstoppable, so these 20 kingdoms came together to stop them. Connecting it back to JoyBoy, you can theorize that his will was imprinted on the Gomu Gomu no Mi fruit, which is why the World Government wanted that fruit so badly.
My last point is that the Celestial Dragons consider themselves Gods, and they referred to their natural enemies as people with the Will of “D”, calling them Devils. Their original enemies were the strong lost kingdom who they would have referred to as devils, since they see themselves as being on the moral right side. Those “devils” created fruits that gave them immense strength, therefore they became known as Devil Fruits. And the people with the Will of “D” are the decedents of the lost kingdom who can unlock more from eating a Devil Fruit because their ancestors were the original creators.
This is my first time posting a theory, so sorry if it’s a little convoluted, I have just been thinking about this for a while and had to share it.