Hi Martin.
This is not a headache with Webinoly. If you create multiple WP sites in a single droplet, Webinoly creates an individual file folder and nginx virtual host for each site. So this way, each site is virtually isolated.
Data Folder: /var/www/domain.com/htdocs
Nginx virtual host: /etc/nginx/sites-available/domain.com
Also, Webinoly creates and configure an individual database for each site.
Please, let me know if you have any issues.