I expect there's not much actual monetary experience of this, as vehicle numbers are low for E63's generally, but the S should be more desirable to some and therefore may sell easier.
You'll get anoraks like me - I had to have mine as it was one of only two S's available in the entire MB network at the time.
With your mileage they look to be around £45k from a dealer so you'd probably have to be a fair chunk beneath that to tempt someone to buy private where they can't part ex, can't get finance and have no come back.