The current description for WiredTiger backups does not highlight specifically which files are used, and the guide could be more detailed. 

See here:

Because we need to freeze the catalog at the point in time when the backup cursor is opened, we cannot keep the WiredTiger.wt in the backup. Therefore, the backup cursor doesn't list it. Instead, the code writes a new file "WiredTiger.backup", and includes that name in the backup cursor file list to be preserved.
Upon startup, WiredTiger first looks to see if a WiredTiger.backup file exists. If it does, it uses the metadata in that file to create a new WiredTiger.wt file (and overwites any existing file). (And then it also deletes the WiredTiger.backup file at that time.)
Therefore, it's expected behavior to not include the WiredTiger.wt file as part of a backup cursor file list; the file should be regenerated at startup time from the WiredTiger.backup file.