Sorry to awaken an old thread, but I'm struggling with S2/S3 right now, and trying to confirm.
I suspect skiwi may have this reversed, in that S2 has the bolt holes flush, while S3 is the one with the front mount 5mm closer to the drive side.
I'm looking at a 2011 Stumpy carbon frame (26" HT) right now, and the holes are flush. In order to run a Shimano FD (which uses the S3/E2) standard, I'm waiting on an adapter (shim/spacer) from Specailized that effectively moves the front mount by 5mm.
Also, the Shimano docs all visually indicate the front mount as closer to driveside, so assming this also confims that S3/E2 a.k.a. "without backplate" is the one that isn't flush.
Similar notes here:
The Front Derailleur (Un)Standard « Tree Fort Bikes Blog
That said, wanted to doubly confim because even Specialized (Canada) was previously unaware of the mount on my specific frame, and was surprised when they ultimately looked it up in their database. Confusion to say the least.
Cheers, thx.