Calibre was always much better at generating Kindle-compatible books than Kindlegen ever was. We use Calibre in our posix-based build chain at Standard Ebooks.
The Kindle file format is just miserable, and Kindle is basically the IE6 of ereaders. Anyone who cares about ebooks should get a different device that supports epub natively. Kobo makes nice devices, supports epub, and uses Webkit as their renderer (when used with their kepub format, which is not ideal but is basically a specially-formatted epub so good enough in the low-bar world of ereaders).
Kobo's also are very hackable, It's easy to get a cheap second hand one, pop off the back cover, swap out the sd card with a bigger one with custom user environments and reader software[1] loaded on it and without any nagging to use a particular store. You can sync books/rss feeds/wallabag saved web pages to it over wifi with calibre. Put a bit of tape over the logo and you have a great white label, no distractions device.