What is your workflow for creating Kindle files? There are several possible routes, including the Kindle plug-in; or exporting EPUB from InDesign, then using Kindlegen or Kindle Previewer.
Have you tried asking on Kindle Publishing Forum on the Kindle website?
I use the Kindle plug-in, but couldn't find anything on the forums I searched. That is why I turned to the Adobe experts. There are problems with epub when it comes to embedded fonts (which I absoutely need), but which Kindle handles perfectly.
Well, you seem to be experiencing the downside of using the Kindle plug-in. You have no obvious way to customize the code. You're dependent on the Kindle engineers to provide what you need.
When you go the EPUB to Kindle route, you get to customize the CSS and HTML before doing the conversion.
Sorry I don't have answer to your dilemma.
By chance, I solved part (1) of my problem, and it was indeed an InDesign thing. I dont know how I overlooked it, but I was using existing InDesign files designed ordinary for book publication to generate the Kindle files, when I should have made a new document and selected not PRINT but DIGITAL PUBLISHING. This puts everything in pixels for better control, In addition, when the mobi file is generated, one is given the option of adjusting margins--something not available if it is a PRINT document.