That's the key argument.
This isn't just a "your word against mine" type of thing. Were this issue true, then it could represent a significant legal risk to Apple.
Categorically denying something that can easily be proven by an external audit (a scenario that they cannot rule out might happen), as strongly worded as they did (excerpt below), would open them up to a huge legal liability in addition to the security issue itself, and for no real upside.
> In the end, our internal investigations directly contradict every consequential assertion made in the article—some of which, we note, were based on a single anonymous source. Apple has never found malicious chips, “hardware manipulations” or vulnerabilities purposely planted in any server.