Indeed, I’m sure most people upload a .docx file and have Amazon convert it to an ebook from that, hoping for the best, and when doing so it would make sense to only consider uploading the cover graphic separately. I’m sure that is where most of the conflicting information comes from online. The Mobi format very much supports embedding a cover image directly in it, and Scrivener follows all of the rules put forth by Amazon to link it up correctly as a proper cover, and from their guide it clearly states you should. Kindlegen will even produce non-fatal warnings if you omit one.
In general it is best to upload an ebook that fits the specifications of the platform you are submitting to, one that is optimised for it. There are several important tweaks for Kindle to the output that Scrivener does, that won’t be present in its ePub format (the starting position being the most obvious).
Another vector of confusion over the matter originates from a bug that may still be around, where the universal MobiPocket/KF8 .mobi file that KindleGen creates can sometimes display incorrectly when loaded directly onto a reader, in that having a cover image offsets the navigation data slightly. It’s not a real world problem however since nobody will be buying your book and getting a copy of it in the format you uploaded. Amazon splits the universal .mobi into two files and only sends the best copy depending on the reader’s device.