1) The SWADE version does include most of the suggestions from the Playing Seven Worlds with the Savage Worlds Adventure Edition document. However it has been refined a bit after quite a bit of back and forth discussion with author. He admittedly hadn't really play-tested the SWADE version anywhere near as much as he had the SWD version. So what you find now in the SWADE version is mostly what was in the document but modified slightly based on my playtesting feedback and with agreement from the original author. A fairly detailed set of notes has been included in the SWADE version to review the changes made (similar to what was in the document).
2) The mention of several rules having been customized refers to things that Seven Worlds modifies from the core rules such as, but not limited to:
- Modified Chase Rules and Space Combat
- Significant changes to how Psionics works, eg custom/modified powers, advancement changes
- Custom/modified Skills
It also includes deviations per above to accommodate using SWADE.
3) Each campaign module actually contains both the SWD and SWADE version. You can activate whichever one you want to use. I have already gone through and made each version 'correct' per which core rules version you prefer. You are still free to modify further, but they should each be playable out of the box for the appropriate underlying core and setting rules, eg SWD vs SWADE.
Hope that answers your questions, let me know if not.
ps. #3 is important since the two are bundled together vs sold separately -- if that isn't clear from the store page description let me know so that it can be updated to be more clear.

