Opt 2 metered water use with unoccupied building

There's no requirement that I'm aware of that says you have to use Option 2 if you have metering in place. You should be able to use the Option 1 calculator regardless of installed metering capabilities. As far as occupancy estimates or default values are concerned, I think you'll likely need an overarching strategy for using consistent occupancy numbers throughout your application, given that several prerequisites/credits take occupancy into account in order to confirm compliance. You might want to work directly with USGBC/GBCI to get an approach confirmed prior to starting your performance period - you wouldn't want issues with occupancy to cause trouble during the Preliminary Review.