They're not as you can see here[1] and here[2]. They both inherit from the HTMLElement interface but div is considered an HTMLDivElement which makes it distinct from a custom element.
<my-element> != <div>
[1] https://developer.mozilla.org/en-US/docs/Web/API/Web_compone...
[2] https://developer.mozilla.org/en-US/docs/Web/API/HTMLDivElem...
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HTMLDivElement has no properties or methods not inherited from HTMLElement. If you inspect the user-agent styling of div versus any non-standard named element, you'll see that they have the same styling path, specifically unlike with span. In other words, non-standard elements and divs are all block elements with the default HTMLElement attributes and methods.
The use of HTMLElement and HTMLUnknownElement for the non-standard elements is to support future additions to the standard elements and enable subclassing down-tree instead of across-tree, which is noted in the spec.