That line of argument is rather misleading, as some kind of content manipulation is inherent to the service an archive that violates paywalls has to provide. It needs to conceal the accounts it uses to access these websites, and their names and traces are often on the pages it's archiving.

Did AT go beyond that and manipulate any relevant part? That's rather difficult to say now. AT is obviously tampering with evidence, but so is Wikipedia; their admins have heavily redacted their archived Talk pages out of fear one of these pseudonyms might be an actual person, so even what exactly WP accuses AT of is not exactly clear.