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I have no idea about Kindle Direct but Kindle Previewer happily accepts epub3 and can convert to mobi/KF8 for use in a Kindle.
As for converting an epub3 back to epub2, that really depends on what epub3 features you used. You had specified a nav. There might be manifest properties in the OPF you might need to delete. You might have to add the correct DOCType to each xhtml file and delete things like epub3 specific metadata and new meta tags with refines, epub3 specific attributes like epub:type, and maybe even epub3 specific html5 only tags like "section".
I think, unless you are familar with the differences between epub2 and epub3, it would be simpler to have InDesign create an epub2 instead of an epub3.
That said, if you keep using FlightCrew/epubcheck to detect and fix things not allowed in epub2, you should reach compliance at some point.
There is no plugin to go from epub3 to epub2 since epub3 can do so much more. But there are plugins like TagMechanic that can be used to cleanup many of the epub3 only attributes and tags. If your epub3 does not use smil, audio, video, mathml, etc, you should be able to successfully convert it back to epub2.
KevinH
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