Thanks romandesign for trying it out - and posting your feedback. Glad its working for you. Even I got some warnings when running since a couple of my mobi files are corrupted (must get around to regenerating/resending them
As you saw, just using "authors": "~ " will only pick up authors, and you can change "~" to "-" or even ""
1. You need to change the sort order on the Kindle to Title - see the Tips section above. At least, it sounds like the issue. This will mean you see all your collections in alphabetical order and then your books. Sorting by Collections is showing the collections in most recently accessed order. Right now I'm not putting a timestamp on the file since I use sort by Title. I'll consider putting a timestamp to sort them initially -but as soon as you access a collection it will jump to the top of the list and mess up your order - which is why sort by Title is nicer.
2. Yes, if you are creating collections by authors then it creates a collection even if there is one other. This makes sense to me - otherwise you won't see your author in your list when you expect to. I'll see if there is demand for this as I don't want to keep adding options unnecessarily.
I'm thinking about providing a gui to edit the collection/ignore names to minimize confusion. We'll see how it goes.