I've search the forum, and it seems than nobody knows for sure. From test that kocur4d@gmail.com did, it looks like Auto-Explore first scan with the Resource Scanner, and then scan with the Survey Module.
So how does that differs from fully automate?
By the way, a suggestion to the devs' team: maybe include in the Galactopedia an explanation of what each of the exploration ship automation does, precisely and clearly. To be frank, it's kind of mind-boggling that more than one year after launch, such basic info isn't included in the Galactopedia or the manual. I know you've been busy, but still...
