How to properly alter a field description in hook form alter
The difference is that $element['value']['#description'] is the description for the property value. If you have a field with multiple properties you can set a description for each property. This is the common practice, but a field widget doesn't have to do it this way. Check formElement() of the widget to see how the element keys are used. Most widgets copy the content of $element to the subkey value, but not all.