The ruling also gives Apple 90 days to decide the exact specifics of how it will comply with the ruling, and until then, the Fortnite app's code would remain out of compliance with the current rules until they are updated within the 90 day period. Since Epic does not commit in their letter to Apple to removing that code, to comply with the rules as they are today, of course Apple chose not to accept them back into the store. If Epic had unwound their willful violation of the rules as they are today, they would have met Apple's stated terms for having developer services restored and likely would not have been asked to wait.
Aside from the guidelines change, does the ruling specifically compel Apple to set aside Epic's contractual violation, or is Apple allowed if they so desire to simply let stand their standard normal permaban for "you knowingly lied to Apple and broke the rules" as the rules were defined at the time?