Standard Folder Structure for Organization Template Schema

llambert1110 

By default Get-SPOSiteScriptFromWeb command will not include folder structure from document library. 

For that you need to update Site Design / Script JSON before adding it as Organization Template. There you can provision folder using list sub action called "addFolder". 

Official JSON Schema for supported action: https://developer.microsoft.com/json-schemas/sp/site-design-script-actions.schema.json 

I have created sample JSON schema to provision folder inside document library:

{
    "$schema": "https://developer.microsoft.com/json-schemas/sp/site-design-script-actions.schema.json",
    "actions": [
        {
            "verb": "createSPList",
            "listName": "MyDocuments",
            "templateType": 101,
            "subactions": [
                {
                    "verb": "setDescription",
                    "description": "List of Customers and Orders"                
                },
                {
                    "verb": "addFolder",
                    "path": "Folder1"
                },
                {
                    "verb": "addFolder",
                    "path": "Folder2"
                },
                {
                    "verb": "addFolder",
                    "path": "Folder1/Folder11"
                }
                
            ]
        }

    ],
    "version": 2
}

Hope it will help to you and if it does then request you to mark this as answer or like it.