You can set what gets downloaded from each download site in Download configuration->Configure Selected Source The button's at the bottom of Edit Metadata panel, next to Download metadata button.
So if you like the tags from Goodreads and Google, but not from anywhere else then you would include Tags from GR & Googs and exclude them from every other site.
If you wanted to do a 'cleanup' you could remove all tags from all books, and then do a bulk metadata download of just the tags from your preferred sources - eg GR & Googs. It will take a while depending in the number of books you have.
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