Yeah, I can see now why it would give off that impression. That feature is going to give them so many issues in the future. I wouldn't be surprised to hear about its removal one day.
Could the difference be that Google associates data with your Google account if you have Web History turned on, but only uses IP addresses in their "logs system"?
If this was the case, IMHO, it would be consistent enough with expectations.
Based on Google's "What Google knows about you" page[1] I would have to conclude that their logs associate your search behavior with your account either way.
That's the doubleclick cookie personalization, which they aren't allowed to tie to your account based on the doubleclick acquisition agreement (which is why "on the web" and "on search and gmail" are separate and why if you go in an incognito window or block doubleclick cookies it will say it has nothing on you).
