It automatically gives you both the mobi7 and KF8 versions (packaged together). And it does give you all the kindlegen source, in a zip file. It is quite easy to unpack and then unzip, make any changes, and then put the revised version through kindlegen again. But once it is fully debugged that should not be necessary.
I don't know enough about using InDesign to make an epub and then converting that for Kindle to say how it compares. What additional work is needed if one uses this method? Does it support all the KF8 features as well as the usual - toc, images, footnotes, hyperlinks, styles, fonts etc.
A publisher can produce the printed book in InDesign, and then also have the Kindle edition as well with no additional work whatsoever.