You can create folders outside of the web folder in ispconfig. The only thing you have to do is to add the path that you want to use in the open_basedir setting of the website.
If you want to allow this by default for all new websites, just add the oath in the openbaesdir default setting under System > server config.
Starting with ispconfig 3.0.5, there is even a default folder for such data preconfigured, it is named /var/www/domain.tld/private
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