I would say that this is a question you should pose to the resort. We were told that the yachts can run any time and this is pretty much a very big pro vs resorts that rely on seaplane transfers.

However, if they'll allow you to check in that early is something that you need to ask the resort. I believe they would accommodate you and let you come over to the resort and if your room wasn't ready you will probably be offered breakfast while you wait. They will otherwise keep you comfortable until your villa is ready. But again, I'd email the resort; I have found them to be quite responsive.

Good Luck and enjoy your trip.