I think that the ATF is more of a user interaction metric than a real Google metric. Their PR team really does a great job at getting everybody's knickers in a twist.
In my own experience with a site which was launched a couple of months ago into beta, having no ads at all improves user interaction and reduces the bounce rate. I'd imagine that if there were ads, a leaderboard above the fold would have a negative effect. Actually, we did have a leaderboard image advertising our launch as a placeholder above-the-fold: removing it decreased the bounce rate.
Consistently low bounce rates and good user interaction numbers have seen our traffic increase every day, more or less, for the past 50 days.