Hi,
Just to clarify that by “Page Number tool” you mean the overlay that appears in the bottom left of the screen? Unfortunately there’s no direct API that you can use to do it in one step. However, what you want is still achievable.
Since you will have a page number overlay in the header. It makes sense for you to disable the built-in overlay by using instance.disableElements.
To add an overlay in the header, you would want to use instance.setHeaderItems. The type of item you want to insert is CustomElement. You can find an example of how you can create a CustomElement item in this guide https://pdfjs.express/documentation/ui-customization/customizing-header.
Thanks,
Zhijie