This is Victor from PageFly - Shopify Page Builder App
Please do not worry about the analytics discrepancies
In reality, there are many factors, such as how different browsers define each action, the customer's privacy settings, and even the customer's internet connection, that can make reaching an accurate number difficult.
About the Shopify analytics that do not work on your site, please make sure that you have not modified the "content_for_header". I suggest you revert the theme.liquid to the version that everything works fine