I see. You're contemplating an environment in which all the ePUBs already exist. In that instance, yes, I can see how this would be very helpful.
In my shop, obviously, we make ePUBs one at a time, and we ship them to clients the same way, with certain very few exceptions, like when a client has several books in production. Having to use this one book at a time wouldn't be a time-saver; it's easier just to use an image for watermarking with house CSS and delete the watermarking code and image than to do this. I mean..it's six of one, half-dozen of another. (We do not use Calibre for eBook-making or conversion). As I said, I can see how exlibris would be useful in a large-scale situation, in which you had a bunch of books to watermark, but when you're shipping 20/books a day, (none all sitting in the same dir), it's probably easier just to have the Crews simply have it in the CSS, I suspect. I'm certainly open to thoughts or concepts of time to the contrary. ;-)