@mobichuck,
I wonder if what you need is a Custom Column in Calibre that displays the collection names as you want them. I'll have a look at the template code if someone else doesn't do it first. Sounds like what you want is to convert SomeTAG~ to __Genre/SomeTAG, and SomTAG! to ___Nonfiction/SomeTAG - that's if I've read your post right.
Have you tried using Genre instead of Tags?
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