You don't understand: The mosquitoes spreading malaria are only active between sunset and sunrise. If you go on tours in rural areas during daytime, there is no risk whatsoever, no matter where you are.
You are right that you shouldn't take chances, and a Hepatitis A shot is a very good idea as is tetanus and diptheria. However, if there was a malaria risk when going on the occasional tour through plantations, forests and mountains, lots and lots of tourists would return home ill. They don't.
As for what happened to this special breed of mosquitoes around Punta Cana: They got killed. And the people working there now have to certify they don't have malaria. Malaria can only spread if there is a host with malaria - in other words, humans with malaria. This is why the risk is a lot larger close to Haiti: More Haitians have malaria.
But again: Travel during the day and you don't have to worry.
Regards, Susanne