I think the confusion here comes from what exactly should be backed up:
In Cryptomator you have a storage directory, where the encrypted data is stored and an access point/directory where you can decrypt&access the data.
I think @Jane wants to backup the storage directory, but @SailReal thought the encrypted data should be backed up over the access point. For the first point you just have to backup all the directories and files of the storage point (where the masterkey file is located). For the latter a custom mount point is the easiest way to go.
We should really add a graphic to the docs explaining this difference.