>So it looks like the correct e3 setting is i-TTL, not >commander, right? p. 146)
Right for what? You haven't described what it is that you're trying to do.
If the flash is mounted on the camera, then the e3 setting doesn't matter (except for the previously mentioned possibility of AutoISO behaving differently with the "CMD" setting...for reasons unknown. There are discussions on this you can research.)
If the flash is off camera, then you must set e3 to "CMD" if you want to control the flash.
If you're using the built-in flash alone, then e3 controls its behavior, and "TTL" is the usual setting.
And of course, AF Assist only works when the flash is on the camera.