You can't really have a modern D over S, because the S is a special proof coin. Back in the day when they hand punched all the mm's at Philly, if a mistake was made, or if a die was reused you could have a D over S or S over D for some business strikes. There's no way a proof planchet with an S on it (the entire coin would be struck), can make it's way to Denver to be overstruck with the D, and, the entire coin would be struck twice, and the odds of it lining up exactly the same are pretty much 0%.
It isn't an "S" because the font is too small, anyway, and it doesn't look like a die chip either. I think it's just an anomaly that we commonly refer to as pareidolia. Chris