Yes - definitely agree that there are better and worse forms of organisation for well-motivated teams. I think the exact details probably differ depending on the personalities of the team (and the nature of the project) - but I'm sure there are generalisable skills too.

As to opportunity costs, I'm not sure about collaboration in general, but too many meetings wastes everybody's time. Time that could be spent Getting Stuff Done.

There's also the principle found in the Mythical Man Month about team-size... after a certain team-size - if you keep building the team (and increasing collaboration) eventually a larger and larger percentage of the time is spent on just keeping up the intra-group communication (ie the activities of collaboration themselves). The opportunity cost there is that you could split into two teams, working on separate things and get a higher throughput.

I also recall reading something (probably by Paul Graham or Joel Spolsky) about the opportunity costs involved in joining a team of people that aren't as motivated or skilled as yourself... the conclusion of the article was that there's an opportunity cost because you're averaging your skill together and coming out with a lower number - and you could be working with people better and thus raising the average (and therefore the payoff from working together).

To address a previous point you made:

But I would have no idea how to organize a project that took major effort from more than 3-4 people

You can do this by breaking the main problem into smaller chunks - and assigning them to smaller teams within the structure. If the chunks are still too big - you just break them down further and so on.

This is how really big software projects work (eg Microsoft Windows) where you have hundreds of programmers.