That's why commutation is a thing. The courts have ruled this as within the pardon powers. His sentence could be changed to reflect something much more aligned with other convictions for the same crimes.
Commutation is not considered during sentencing or mandatory minimums or anything like that. It's only an option for very popular cases and even then it's rare.
It’s not expunged but you have a letter from the president saying you shouldn’t have been convicted in the first place. The meaning is different even thought the legal outcomes are the same.