From the Washington Post article linked in the OP:
Apple hopes to bring Amazon into what could be a weeks-long hearing at the U.S. District Court of the Southern District of New York in Manhattan, saying documents currently redacted by Amazon are “potentially embarrassing” and show that the retailing giant had also considered the same pricing model that is now under government scrutiny.
This is the same misdirection that was being used for defense in the original filings. It is not the agency model that is illegal, so there's nothing wrong in Amazon considering using it. It's the collusion to bring about an agency model that is the subject of the antitrust suit.