Apple has clearly overreached, but this kind of remedy is not about restoring competition.
This is about Apple using its retail outlet to advance and profit from a conspiracy among publishers to jointly set the terms on which they sold to retailers, including retail price fixing as the key focus. Insofar as it is about "restoring competition", its about restoring the need for publishers to each seek separately to make the best deals with retailers, rather than unilaterally imposing common terms. (This affects retail prices, but its not about retail competition.)
The remedies which benefit other retailers aren't about restoring competition, per se, they are about remedying the harms done by Apple's unlawful activity to other market participants. In Amazon's case, that also happens to reward the incumbent major player, but then, Amazon was the primary target of the illegal conspiracy. So this is not inappropriate.
As to your allegations against Amazon, if one assumes they are true, they might be a basis for anti-trust action against Amazon, but they aren't an argument for limiting the remedies imposed on Apple for conspiring with publishers in a price-fixing scheme.
That was the case, there was an investigation. All the publishers quickly settled because they were caught colluding to use Apple to force Amazon to switch sales models.
If Apple is forced to sell Amazon's books, Amazon should be forced to sell Apple's books on the e-ink Kindle.
The argument that Apple did something wrong therefore a destructive remedy is justified is absurd because it harms consumers even further by damaging the competitive market even more.