I have built a custom Sharepoint Top Application Customizer Extension for a branding project, does the Top Application Customizer always appears on the top of the page? as per our requirement we are manipulating the css on the page and hiding the OOB menu, and replacing it with our custom menu extension which I feel a workaround or hack. Is there a way to disable the OOB menu programmatically? also how the Top Application Customizer works with the Hub site? please help me on the better way of implementation of the Top Application Customizer.

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You're correct. Using CSS to hide out-of-the-box sections of a modern SharePoint page is not supported.

The application customiser will work with a hub site (since it's just a modern SharePoint site).

If you remove all the links in your hub site navigation and set the hub name to "Hidden in navigation", then you will be left with an empty bar and no navigation.

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