Yes, it will work in Plan mode also. Plan mode and Autorun use the same settings that you've entered for EAF autofocus. That's been my experience with both the Air and Air+.
I think that Plan mode is generally considered a form of Autorun. There are statements that guiding logs are only generated during Autorun, but they are also generated during a Plan sequence. As you noted, the information in the manual is outdated, I.e. written before Plan mode existed.
-chuck-