The commission in the Everton case said that the failures by Everton are so serious that a sporting sanction must be made. Everton argued that a financial sanction should apply and would be fairer.
The commission said that if they applied only a fine, the owners would dip into their pockets, pay off the fine, and Everton would be in no worse a situation. But Everton benefited from their non-compliance by having a stronger team, getting more points in the season, and avoiding relegation. The penalty needs to include a real deterrent, otherwise clubs in future would just ignore the rules in order to avoid relegation. Hence the hefty points deduction.
In future, the PL wants cases to be judged and punished in the season in which they occur. This is an honourable objective, but as the commission pointed out in the Everton case, this objective should not be allowed to hamper a club on its defence against charges.