I would imagine that when there were objections to the originally proposed route, the government said "To hell with them then. If they don't want the bypass we'll keep the money."
A great shame in my view, because if they could have found a way to use the proposed route without damaging the lagoon (such as raising the road) it would have been a great boost to Cabarete while being far enough from the main town not to disturb too many people. The original plan also included renovating the main street to be more people-friendly, which now presumably won't happen either.