Informed speculation based on the quotes in the article: it appears that Hachette accepted the "incentivized agency" terms that Simon & Schuster agreed to, which is very similar in structure to the terms Amazon offers for Kindle Direct Publishing.
These terms give publishers a strong incentive to keep book prices between certain thresholds (for KDP, higher margins if the price is set between $2.99 and $9.99), but Hachette has the ability to set prices outside of those thresholds as long as they're willing to accept lower margins.
Hachette gets nominal price control, and Amazon gets their preferred pricing because Hachette will get smacked in the pocketbook if they choose to exercise it.
These terms give publishers a strong incentive to keep book prices between certain thresholds (for KDP, higher margins if the price is set between $2.99 and $9.99), but Hachette has the ability to set prices outside of those thresholds as long as they're willing to accept lower margins.
Hachette gets nominal price control, and Amazon gets their preferred pricing because Hachette will get smacked in the pocketbook if they choose to exercise it.