Site collection app catalog can be enabled using SharePoint Online Management Shell or Office365 CLI as mentioned here.
is there any other way if I have Microsoft graph token or SharePoint rest api token with correct permission ?
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DevÁsith
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The short answer is no.
For graph api, there is only read endpoints for site resources in Microsoft graph API, we cannot create sites. Please check this documentation: Working with SharePoint sites in Microsoft Graph
For SharePoint rest api, we can only create modern sites collection. There is no ability to create site collection app catalog.
https://learn.microsoft.com/en-us/sharepoint/dev/apis/site-creation-rest

Michael Han
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