Yes, you are right, but under the installation of WebsiteBaker there are also these "subfolders" that are needed independently of the server subfolders.
I suspect that it has to do with your "outdated" rights assignment www-data user versus ftp-user (that's how it used to be done) On my server I can't select that at all. They work with Fast-GCI or something like that.
If I remember correctly there was a "php-user" and a "ftp-user" with different rights.
This problem does not exist anymore with "Fast-GCI".
Here is an example
-my server area
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