I'm pretty sure Funko used their service in good faith and didn't know it's based on over-aggressive AI bullshit. They're still on the hook for picking a bad company to partner with, but I don't think they intended to take down the entire domain.
Former employer worked a little with Funko and Disney, and it was pretty comparable. I don't see what Funko has to offer other than Licensing IP and strictly enforcing their own. Based on my (limited) experience, I doubt they chose this service by accident.
I don't see a large message on the Funko site with a profuse apology for taking down Itchio. This indicates to me they fully endorse their action and are not willing to make amends.