It’s worth noting that since this thread was active, Amazon no longer recommends using Mobi anywhere in the production chain, not even to load into Kindle Previewer. Amazon now encourages everyone to use ePub, and you should make sure your copy of KP3 is up to date as well (as it should be warning you about this when you load .mobi files).
Thus the workflow from Scrivener looks no different than most other tools these days: make an ePub file, load it in KP3, proof the layout, and if it’s good, send the original .epub file to KDP for upload.
We do leave the Mobi compile option in the software because, while Amazon no longer supports publishing with Mobi, they also have yet to create any kind of alternative for sideloading to devices for more extended proofing sessions. The last time I asked them about this, they honestly expected authors to be sitting up at their desk in front of Kindle Previewer for 500 pages. They have no solution for proofreading, because their devices and software cannot read ePub.
If the quality of the Mobi they are producing via KP3, at the behest of Scrivener, is not to your liking, then there are probably better conversion tools out there these days, like Calibre. For proofing though, I’m not sure how important some of these additional features are like advanced typsetting, so long as looks pretty close to how it’s meant to in the end. If you need pixel perfect accuracy then that is what KP3 is for.