I am confused as to whether the Sanctuary is meant to be unique or not.

On the one hand, it says that it is unique in the Craft & Construction tab, and you cannot build a second one after building a first.

On the other hand, upon clicking on its name in Buildings, it asks for the quantity which you wish to use. Even after asserting the use of only one Sanctuary, the next page also reminds you that only one Sanctuary is being used, and asks for quantity once again.

If the Sanctuary is meant to be unique, it shouldn't ask for quantity, or reference the quantity of 1 in any particular way. If the Sanctuary is not meant to be unique, it should allow multiples to be built.

Which is the case?

I believe that attempting to craft another Sanctuary would result in an error, and what you are experiencing might be coding that was edited to be used for the Sanctuary from something that allows you to craft multiples (such as climbing gear). Since sactuaries are limited to one, you will be unable to create another.

There's a single template for crafting, and single template for using items. You won't be able to craft several unique items or use more than 1 item if you have only one. Any building is unique.

See? ^ even I needed to learn hehe