I've been reading that thread, but not having a Kindle, it's hard to even discern what difficulty you are having. Are you saying you directly access Calibre's Library folders, or just that you prefer Saving to Disk first, then drag/drop? I find it hard to think of any circumstance where direct access is preferable. I've only recently been able to convince Calibre that my phones are true ereader devices (I have Charles to thank for that recent improvement), so I've been using Save to Disk for a long time, followed by drag/drop.
Before I figured out how to use Calibre, I tried to drag out of the Library directly. That's a lousy method. It's hard to find the book, it has the wrong name, it takes a million clicks to get all the series I want, then I have to fix the names, put the files in the right folders etc.
The right way is to just set the output template to the name you want, then use the GUI and search for all the books, select, right-click and Save. It gives them the correct name that I
want and puts them into the correct folder I need
without regard to what Calibre has used for its Library. I typically saved to either desktop or direct to the SD card.