I am having a little trouble understanding but it seems you are asking whether to list the master bedroom as a private room or as an entire house listing due to you not being there during the guest's stay even though the two other bedrooms are closed off?
If so it kinda depends... Entire listing is a more attractive reservation, can usually book for a higher price and you might get you more bookings. However you might not attract good guests who are purposely trying to book an airbnb with the homeowner out of their hair. Unless you have front door security or are willing to vet your guests, I would just list it as a private room and let your guest be extra happy to learn that they have extra privacy.