I believe when it comes to iTunes' chart, the keep editions segregated. If you watch, you'll see the " (Deluxe Edition)" of albums on the charts when there's a non-Deluxe available and such. That's just speculation on my part though, as I don't really keep track of iTunes.
However when it comes to Soundscan... not entirely sure. I know with Killer, the Explicit and Edited version of the album was handled separately (the edited version sold like 250 copies, Lol). However when it comes to exclusive versions for Best Buy, FYE, etc. I'm not certain. Given the numbers, I would assume that they're all rolled into one. However, they each had their own barcode which would suggest they may be treated separately by Soundscan. I don't know.