On the day after her I-94 expired, she would have immediately been out of status and subject to deportation. ...until the day a proper I-485 package was filed. Once the proper package was submitted, she would have been granted authorized stay in the US. Authorized stay is not a legal status, but it halts accrual of unlawful status until adjudication of the I-485.
Waiting 90 days delays the entire process of being able to work, leave the US, getting a Green Card and becoming eligible for citizenship. As @Daphne . stated, there are no benefits in waiting to file for adjustment of status.