Why not? If it’s good enough for the government, why isn’t it good enough for the company they are going after?

It’s bad for both. But this thread is specifically about Amazon.

It isn't "whataboutism". If the government's position is that MFN terms for vendors are fundamentally anti-competitive and bad for consumers, which I agree with, then it raises questions about any organization or sector of the economy that widely requires MFN terms. It discredits the FTC when the US government routinely engages in the same market malpractice that they are accusing Amazon of but are disinterested in changing their own contracting behavior. It doesn't become less bad because it is the government doing it to vendors instead of Amazon.

This "rules for thee but not for me" behavior is why trust in government institutions has been eroding. It is difficult to give good and necessary actions the aura of legitimacy required for democratic institutions to function when the hypocrisy is obvious.

Common law is basically whataboutism. Whataboutism isn't inherently bad, it's not always a deflection. It is reasonable to expect similar treatment for similar actions. If anything, reciprocity is one of the very foundations of society and of our justice system. You can't really discuss a lawsuits without talking about precedent, it's inherent to the discussion

(In a way it's amazing how shouting whataboutism is now more often used to deflect or excuse double standards and unfairness than whatboutism itself.)