Thanks for the info.
In case it motivates you to fix it, I'd like to explain why I'd use it. I keep a custom column with the original filename of my Amazon purchases which I use as my save template. This allows me to simply overwrite the old file with my calibre copy that has corrected metadata, and preserves the annotations for the book. Additionally when I delete a book from the device UI it leaves the annotations files behind allowing me to simply re-add the book from calibre and have my old annotations.
For this I rely on a stable save filename. It is easier if this is the filename Amazon uses as well, since it works with both Amazon and non-Amazon books and I can redownload the annotations from Amazon if necessary then just update the book by overwriting.
So I'd appreciate an enhanced add option -- but I understand if it's not worth the time to implement.
calibre is still awesome, and I have it all working smoothly albeit with a little more effort than my laziness requests of me.