Thanks for bringing this up. I'm the OP. Please note my response to a similar comment below: https://news.ycombinator.com/item?id=5416724
You're right that the logo is not only below the fold. There is a dimmed version in the top right corner, but the point where I really introduce the app is below the fold. I admit that the title is slightly inaccurate because of that. It just made for a snappier headline.
The main point is to place the logo low on the visual hierarchy. The dimmed logo you are referring to is not very obvious. Visitors will read the headline before they see it.
Also note, everyone is noticing that occurrence of the logo right away because I explicitly point out the prominence/location of the logo in the post. If you were visiting the site without that context, you wouldn't notice the dimmed logo.