I'm curious if this is more a consequence of the medium (internet/phone) and its lack of tools or this specific goal (developing software). I would imagine that it is easier to build a friendship through, say, playing World of Warcraft together than pair programming. Perhaps this is because software development tends to be a more solitary activity and we're slower to accept others in it.
One of the surprising things we've learned while running Hacker School is the extent to which your comfort level dictates how much you will learn. To learn effectively, you need to be able to ask questions without worrying about looking stupid, you need to be able to admit when you don't know something, and you need to be able to jump into things that are over your head and know that you'll be able to figure them out as you go. Your ability to do all of these things is related to how comfortable you are with your environment and the people in it.
When I wrote about the situations where people build friendship, comfort and trust, I wasn't thinking about pairing sessions (though it can happen there). I was thinking about all the other things you end up doing when you're in the same place with a bunch of people for an extended period of time. Comfort gets built during group lunches, on the weekends, at movies, concerts, in the park, at bars, the beach, etc. Hopefully this clears things up a bit.
EDIT: "talking" -> "thinking" in the second paragraph.
I just touched on the development aspect I found interesting, but I understood the underlying intent: the "other" things. I agree about group lunch being very important for developers working together as one. I've experienced both sides of the coin and there is a discernible difference in relationships/familiarity between the two. I'm curious if this group setting can ever be replicated virtually. I don't think Soylent IV & Skype will do the trick. :)
I'd love to see a postmortem blog post after the next class from both students and maintainers and what did and didn't work with the virtual program.