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Both of your work flows would work. As long as you are generating collections.json out of the final book destinations in /documents folder (as they exist on kindle) you should be fine. Each sub folder under /documents will become a collection name.
As far as making Calibre work with this.
If you're using Calibre to save your books to kindle. Best way would be as you describe. Copy all books from kindle as they exists in kindle file system. Reorganize folders to make them "collection names", then run dir command on that folder structure. (Make sure all kindle folders are under "kindle" folder on your pc). This guarantees file paths will match. Then copy the generated collections.json file.
There may be a way to set up folder destinations of your books on kindle using Calibre. This would allow you to set up folders as collections while moving books to kindle in one step.
Make a back up of your existing kindle collections.json file and start with few files at first. These files should show up in your newly created collections.
As far as this being web only solution. Some may see this as an advantage over software installed on your pc. You can use this on multiple pc's without installing software on each pc. It's cross platform etc.
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