I always convert those to ePub to do the changes - but thats more of a habit I suppose. In both of our cases Calibre also stores the original file as an untouched copy - which frankly is the most important step.
But yes - I understand why you would do it.
As you see I come more from the "production side" of things - where it makes very little sense to treat Amazons file formats with any additional attention for detail.
(It only would be a "value add" for Amazon - and honestly, why should we become more invested into something that by definition was created to be "something proprietary for them"...)
You make sure, that most of your .css stylings make it through the automated conversion, and thats it. Any additional time you put into them, essentially is lost.