I have a clean InDesign 16.1 document - no bounding boxes anywhere on text or images. I have created object styles for key html content: object styles are named the same as the html. I do not have bounding boxes on anything, and everything displays properly in InDesign and epub.
If I leave mapping as automatic, or set to div, there are no bounding boxes in the epub. But as soon as I map section to section, figure to figure, and figcaption to figcaption, the epub version adds bounding boxes around the content. This does not happen when I map text to text.