Thanks for all the feedback; good requests.
Specifically you meant he .HYPE_element_container elements in the DOM? Specifically it was to work around some issues with 3D transformations and give consistent perspective to elements. I have been wanting to try removing it recently, at least for non-3D elements. It is a pain for me as well in debugging DOM issues!
If you're asking about embedding the *_hype_generated_script.js, this is an option in Advanced Export as "Inline data+loader" and Export Scripts as exportShouldInlineDocumentLoader. Export Scripts also have an option for exportShouldInlineHypeJS to inline the runtime, but this is a little different as it includes a specific script tag at the top of the document. Technically you could paste the HYPE.js runtime at the top before anything else is loaded, but make sure this is the full (physics+IE) version.