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You aren't wrong in that both Kovid and I were talking about the individual metadata screen.
To be honest for the level of granularity of overwriting you say you want, treating each book individually is pretty much the only way it is going to work anyways. How else can it work? You select a bunch of books, and hit ctrl+d. Now you are saying you want some sort of opportunity to review the results before applying them. So you are going to need screen(s) to one by one compare all of the fields retrieved with the current value of each book. That isn't significantly different from what you are doing by using the Edit Metadata screen. The only difference is one less button click on Fetch metadata per book (you do know you can use the Skip button to stay "in" the Edit metadata screen to move to the next book, right?)
Don't get me wrong, I rarely use the Edit Metadata screen myself and mainly use Ctrl+D. But I don't ever get myself in a situation of metadata being "overwritten". When the book is added to Calibre, the only metadata it will have for me is title, author and (sometimes) series. I disable the metadata download overwriting title, and author I sometimes disable, sometimes not. For the rest there is no data to be "overwritten".
If it is an existing book that does have metadata and I only want a partial field updated (like Rating), then I only enable that checkbox in the metadata options. That is why I asked Kovid to add Select All/None buttons, to quickly toggle those settings.
As for covers - well I usually use my Search the Internet plugin to find the best possible cover one by one anyways, and so would make sure I click on the "Download metadata" button rather than "Download both".
Using bulk download is simply the wrong operation for you to be using if you want granular control over which books get updated and which don't. Filter/sort your books to just the ones you want to update, select the first, do your fetch, click Skip and repeat for the second etc if you need that.
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