Hi @Amagoia Cormenzana ,
Modifying a standard template site in SharePoint using the SharePoint Management Shell is not directly supported.
As a workaround, you can create a new custom organization template from a site created using a standard project management template, add 3 lists to it, and save it as a template.
When you save a site as a template, any lists and libraries, look and feel, and other objects such as calendars, etc., you have added are also saved, optionally with content.
Please refer to the following articles (The Save as Template feature is hidden by default.):
https://www.sharepointdiary.com/2017/06/sharepoint-online-how-to-save-site-as-template.html
https://www.sharepointdiary.com/2017/06/sharepoint-online-save-site-as-template-missing.html
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