Strange, I've used Calibre to convert my amazon.jp purchases and am pretty happy with it. It does convert vertical text into horizontal text by default, but the resulting text is perfectly normal without the problem you described, and you can add CSS to force vertical RTL.
There's some example and the css code they used towards the bottom of this page, if you'd like to take a look: https://webnetforce.net/post-105/
There's some example and the css code they used towards the bottom of this page, if you'd like to take a look: https://webnetforce.net/post-105/