I use Amazon's conversion tooling rather than Calibre (first kindlegen, now amazon.com/sendtokindle), and haven't noticed any formatting issues - and the website gives me wireless sync support too. No arbitrary TTF support or custom screen images, though.
Well one of my Kindles is actually a DX, which can only communicate via 3G which has long been shut down, meaning that the only way to send books to it is via USB, so I don’t think the sendtokindle would work with that.
I also wouldn’t want to use a cloud service if the books are obtained from an, uh, “unofficial” source. Again, not that I would ever do that, because that would be a crime.
I use Amazon's conversion tooling rather than Calibre (first kindlegen, now amazon.com/sendtokindle), and haven't noticed any formatting issues - and the website gives me wireless sync support too. No arbitrary TTF support or custom screen images, though.