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My own process of tagging is identical to yours - use the metadata sources to get some tags and then replace with my own if needed. As I only use the Goodreads metadata plugin for tags and that is customisable to a certain extent it is less work than it used to be.
I don't have an interest in writing such a plugin myself as you describe. However I suggest there is an arguably "better" way to do what you want. Just use the Tags column for downloaded tags, and add a custom column to store your own tags in. You could put the original column off screen, and have it visible in the book details panel where your comments are if you so desired.
Requires no plugin and no mucking around with the comments field.
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