You may certainly use the Premium website Builder to create your base site and when you are ready, add other components such as a shopping carts or moodle.
All you would need to do is to install the other programs into their own subfolder (such as youdomain.com/shop or any other subfolder you wish). This way it would not interfere with the existing pages of your main site.
Then, you would simply need to integrate external links to the other program pages from within the builder to their respective subfolders.
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