"To calculate average position, we take into account the top ranking URL from your site for a particular query. For example, if Janeís query returns your site as the #1 and #2 result, and Davidís query returns your site in positions #2 and #7, your average top position would be 1.5."
Not quite sure what to make of that...
I understand what this means - that if one query returns the same site as a two (or more) separate results, they will take only the top result of this query for their average calc.
So in their example, Jane searches for "widget" and www.example.com/about-widget is #1 and below this there is www.example.com/widget-cost at #2, then from this query they will only take position #1 towards average.
David also searches for "widget" and he gets www.example.com/widget-cost at #2 and www.example.com/widget-photos at #7. From this query they only take position #2 towards average.
Then average ranking would be calculated as #1 + #2 / 2 = 1.5 (assuming they use aritmetic average).
However, I observed that if you have for example 4 photos above the first organic ranking then the organic ranking would be recorded by Google as #5. The same is if you get mega sitelinks. The "second" organic listing is recorded by Google as position #8 (Google counts first listing + its 6 mega links as first 7 positions).