No there is no way of determining which are calibre generated covers. A cover image is just an image. At best you can detect (using QC) whether a book has had a cover page added to it by calibre - but that cover page might have an auto-generated image or it might have a genuine image.
As to running in bulk - sure, just select all the books you want to run it it on and generate. Of course you can only apply one "setting" to the selected books - i.e. if you wanted to have different looking covers for different genres you would need to filter your selections to just the relevant books and generate for each subset.