Maybe it's simply a difference in awakening. The permanently fused ones may have relied on their abilities too much and the fruit overcame them, leaving them as permanent freaks. Maybe the same thing awaits Sheepshead down the line.
I assume it's the different stages of development in CC's Smile research. At first, the Smile user would simply merge with an animal. Then, as CC was making progress, they could partially activate body parts of the Smile animal and lastly, nearing perfection of the Smiles, they would function like authentic DF's.