Not sure how that would negate the fair use defence.
If the companies had bought all of the ebooks, then they might be in the clear.
Or is it "you did a bad thing in the process of making another thing but we can only punish the initial act"
Yes you can create a transformative work but if you can get it to make an exact copy and can't get it to stop doing that I would say there's a problem.
if your a service provider and I send you a DCMA request how do you handle it?