They need to resolve their own buggy UI, I don’t want to set some arbitrary padding to compensate for that. If they ever change the Figma UI then the padding becomes inaccurate again. One simple solution is to make the Figma UI take a fixed amount of space and offset the prototype for that amount - no overlaps or padding requirements.
I’ll just leave my related bug report here: [Bug] Figma prototype UI obscuring fixed website header