Having reread this thread, it seems to me that you get most of what you asking for with the following:
1. Define a set of tags for your workflow. Make them unusual and make them have a common prefix, such as WF:done, WF:step1, WF:step2, WF:notapplicable, WF:in_process
2. after importing books, search for (assuming the above tags) 'not tag:WF:'. This will find all books that do not have a tag with WF: in it. Select all the books, then use the bulk metadata editor to add WF:step1 (or what-have-you) to the books. Once saved searches are available, you will be able to select this search from the searches box or the tags pane.
3. When you process a book, change its workflow state using the bulk metadata editor instead of the single book metadata editor. The bulk editor is capable of adding and removing tags without needing to see/avoid all the other tags, and its completion mode makes it easier to identify the tags you wish to add/delete. You would remove the current step tag and add the next step tag.
4. You can set multiple tags to indicate substeps. For example, when you decide to start working on a book, you can add the WF:in_process tag without removing any other tag. This way you can rapidly find all the books that you are currently working on.
I understand that this doesn't define a real workflow system with nice buttons to move the book to the next state, and also that there is some typing involved to change states. It does (I think) solve your folder problem (where are the new books?) and partially solve the 'lots of clicks and tag editing' problem (bulk editor changes editing all tags to add/delete individual tags).
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