I am using version 2.7 of Scrivener for Mac OSX (10.9.5) and have formatted a novel using manuscript format with the following font specs: Georgia 12pt, line spacing 1.5, text justified right and chapter titles in Arial 18 pt. When I compile to the Kindle ebook format, all of the left sided indents are lost and the entire document appears to be justified both right and left. If, on the other hand, I compile to ePub format all is well. Since my ebooks are destined for Amazon, I suspect that the Kindle format would be the most appropriate. Oddly enough, if I change the body text font to Courier the indents are retained. Is there a problem with the Kindle ebook generator and the Georgia font?
All of the formatting attributes you listed are things that you are supposed to avoid when creating a Kindle book for Amazon (they have a long publication guideline PDF with the details if you’re interested). In summary they want body text to be uniform and easily adjusted by individual reader preferences, which includes justification (on newer models), line-height, margin width, font size and font family. If the reader prefers to read your book in a sans serif font then it is their choice to do so.