Submitting an eBook to Kindle Direct Publishing

Scrivener make good looking ebooks in MOBI format that are easy to test locally with Kindle’s viewer.
During Amazon’s submission process they don’t accept MOBI formatted files. They accept DOC, HTML or EBUB as I understand it.

What does L&L recommend that an author submit for a Kindle eBook, since Scrivener can output all three?

I haven’t gone through the Amazon submission process, so take what I’m saying with a grain of salt, but my understanding is that which format you submit to Amazon for their toolchain to process really depends on what kind of material you’re writing to begin with and how it’s formatted. That’s the reason Scrivener can output in different formats – each one has its strengths and weaknesses, and it’s up to you to figure out which one is going to work best for you in the given situation of YOUR work and YOUR data.

KDP does accept properly engineered MOBI files…

Scrivener complies fully with KDP’s MOBI requirements.

I have submitted both epub and mobi format. Both worked equally well.