Things change. Used to be you didn't need a neutral in a light switch. Now you do.

Used to be you didn't need a neutral in a dryer plug. Now you do.

Used to be you didn't need bond wire in emt. Now you do.

Code changes. Constantly.

The point is that cutting wires flush to the box doesn't help anything, it just means now there's a hindrance in the future. Maybe code changes in the future. Maybe a future person living in the house wants to do something else with that wire, but now they can't, bc an important wire is snipped.