Like I said, I don't have an Android device, so I'm not sure how everything works.
I'm guessing it needs to be rooted because you still don't have R+W permissions to the root file system even with Astro right? I know you can do whatever with your SD card, but the Kindle program itself is not stored on the card, and I would assume that the covers are stored somewhere in the main storage, and not on the card. I could be way off base though lol.
As far as having the same title as an kindle book that Amazon sells, it really doesn't matter. Amazon doesn't even look at the title. It is looking for the ASIN number which is embedded in the .mobi file.
See this thread for reference
So basically AFAIK, the Kindle app just searches for a cover from Amazon depending on the ASIN number.
This is pretty easy to inject into the file though with mobiperl.
I wrote a script to automate the process here