Bonnett Creek Resort is not affiliated with Disney at all. It's surrounded on all sides by WDW property, but the property is not owned by Disney.
The story I heard about it goes thus:
Back in the 1960s Walt had his people secretly buying property for the Florida Project. But there was one holdout who wouldn't sell for some reason. And when the news finally broke, and surrounding land shot from $180 per acre to $1000 per acre, Disney had already bought enough land to build the project. The holdout parcel was on the southeastern corner of the property, anyway, and it was expected that DIsney would probably be keeping those outer areas undeveloped for a long time, to block out the outside world from intruding on the park. So they left it alone and never bought the parcel.
Fast forward almost 40 years, and that last non-Disney parcel has changed hands at least once. It's prime real estate, smack dab in the middle of the biggest, most lucrative tourist destination on Earth. And somebody was finally able to broker a deal to build a resort hotel on that land, which eventually became the Bonnett Creek Resort.
I don't know how accurate that story is, but it fits the facts and makes sense.