Differences between Org Chart version 3 and version 2
Org Chart version 3 was released in September 2017. This is a new major version with a different installation process.
Org Chart version 3 is a SharePoint Framework solution. Thus, it can be used on “modern” SharePoint page as well as on “classic” SharePoint pages. SharePoint Framework solutions are not supported in SharePoint Store. The only way to install version 3 is through your SharePoint App Catalog. It is not required to install the add-in from SharePoint Store anymore. You can find more information in the installation instruction.
All improvements from previous versions of Org Chart for SharePoint 2013/2016 On-Premises up to 2.3.7 are migrated to SharePoint Framework version.
There is no automatic upgrade from version 2 to version 3. You just install the new version and replace the old web part with the new one.
The previous version 2 is still supported, you can install the add-in from SharePoint Store. On the default add-in page, you will see instruction for installation of version 3, but you can navigate to version 2 by clicking on the link as in the screenshot below: