The tool uses the build information to detect what assets has been included or not, so you can select all the scenes you want by adding those to the build.
It does not require 4.x to work, I don’t know why it came out that way on the Asset Store, but it should be fixed by the next release.
This looks extremely useful, so I purchased it to help me slim down a project that’s grown to 14GB. I did a build, then choose the tool from the Assets pulldown. It spun for a bit, then Unity crashed. I relaunched, did another build, same thing. I had just restarted my computer, which has 8 GB of RAM. Is that simply too big of a project for it to process?