All Sigil can do is help you create a spec-compliant EPUB. If certain renderers display things differently (or if Kindlegen introduces unexpected results on various platforms when converting EPUBs to Kindlebooks) then you need to look to those knowledgeable about those particular renderers and conversion tools for help.
The Workshop or the Kindle Formats forums might have better insight on what special considerations an EPUB that's going to be converted to a Kindlebook might require (or what's even possible). Sigil certainly might be able to help you with those requirements once you know what they are.
EDIT: unless, of course, someone has a short, magic solution to this specific problem. In which case, feel free to tell the OP what they can do with Sigil to overcome it.