There certainly are a lot of issues to be addressed if such functionality were to be made generally available, but in my own case, doing it manually is inferior to doing it automatically, and I know this because of the pain I went through after switching from B&N to Amazon.

A big reason why I've never bothered trying to make this a more general solution (perhaps via a plugin) is precisely because it fits a certain workflow, i.e. mine, and would be hard to generalize. However, within that workflow, this has been an extrordinarily useful feature. If I'm reading a book that I purchased months ago and notice that there was some problem during conversion when I first imported (let's say spacing was too-aggressively removed between paragraphs, so it included scene breaks, too), I can just go to the book, hit “Convert”, make a small change, and go. Calibre does the right thing, too and uses the ORIGINAL_ format for conversion if one exists.

Basically, this tweak makes things a lot easier and less error prone for me, but that's because it's tailored for how I work.