Liesse,
The Edit Collections feature was mainly put in to allow you to edit collections on the Kindle that you didn't manage by Calibre - e.g. like a Currently Reading list you want to update on the Kindle and via the plugin. But it can be used to manage all the collections. Not exactly what was intended, but if it works for you great
You can use the Preview mode to see what collections will get created without causing any changes to your collections. Play with the customizations and then hit preview. And if you do save the collections and change your mind you can restore the old collection file (but only the most recent one). You can also manually make a backup of your system/collection.json file just in case as well.
Tags really are pretty useful - and designed exactly for what you want. But I know a lot of books bring in their own tags which can make things a bit confusing, although there are ways around it. One step at a time. The main Calibre forum and Library Management subforum are always open for help and tips
Glad to see you like the collection count for books - I figured it would save a lot of looking around for books not in a collection. I'm working on improving the View Collection report to show books in collections and not in collections, and also making sure all the books in the Edit collection window have a Title and not a path name in some cases. Periodicals have been the biggest challenge, but I think I've got a handle on how to count them and identify how many Periodical Back issues there are. Its not really needed, but I'd like to be complete
Shame we can't see Archived titles or the names of the internal Kindle files.