There’s an option in the File > Advanced Export… panel in v3.5+ that is “Inline data file+loader” which will inline the *_hype_generated_script.js file into the exported HTML. This option is exposed to Export Scripts as the "exportShouldInlineDocumentLoader" key; check out line 185 of the DoubleClick Studio.hype-export.py to see how it is used.
There’s not presently an option to inline the HYPE-XXX.thin.min.js/HYPE-XXX.full.min.js and HYPE-XXX.waypoints.min.js files since they are dynamically loaded based on need. However, you could include these in the head yourself safely if you have the contents of the full runtime and the waypoints script. This could be automated in an Export Script.
As for CSS, Hype dynamically sets this on elements in the runtime, so there’s no CSS needed to be inlined.
Does that help?