Hi,
Thanks for contacting.
As you know some HTML elements can’t be wrappers. For example, you can’t have put a <div> element inside a <span> elements in some browsers.
The tooltip plugin generates HTML based on the tooltip contents and its options, it’s possible that the generated elements can’t be wrapped with your custom HTML and the browser moves the code outside of the wrappers.
To change the styling and other properties of tooltips you can use their generated CSS Class/ID.

The above image shows the generated tooltip CSS Class/ID for a test tooltip.
Use Browser Console to view the generated HTML.
Thanks.