The challenge really is setting these things up from an early stage. I don't think as a founder at a company that has not yet been funded you have the luxury (time, brain power, etc.) of thinking about these things, you're so busy trying to get the company off the ground that everything else is secondary. Even more so once you get funded, because all of a sudden it's not just you pushing yourself, it's a group of investors that are all of a sudden breathing down your neck (not to say all are like that or that it's a bad thing...) Especially if it's the first company you've founded and you're stumbling along, the learning curve is exponential...
"I don't think as a founder at a company that has not yet been funded you have the luxury (time, brain power, etc.) of thinking about these things"
Agreed, albeit to an extent. It's one of those things that must be taken into consideration, because the magnitude of the downside is so potentially massive. But to a large extent, 100% agree with you, it's not something you have the luxury to ruminate on for any appreciable length of time.
Ergo, I'd suggest that the time to do the rumination is whenever a big org shift or financial event is on the horizon (major funding round, new board appointments, major new hires -- especially if there's any overlap with your own responsibilities -- etc.). Each major shift of this nature deals some new cards, and it changes everyone's hand in the game. It's helpful, if nothing else, to take stock of how things will change for everyone before the change takes place.
[Of course, I'm not suggesting that founders become preoccupied with this sort of thinking. That's a recipe for paranoia and a poisonous political climate, and it may end up creating a self-fulfilling prophecy. Rather, all I'm suggesting is that some nontrivial degree of thought be taken.]
Come to think of it, there was a great article on HN about 6 months ago about how to structure a founders' agreement. It seems especially relevant to this conversation. Wish I could remember the title or author.
That may be true in most cases. However I think that founders who have significant financial accounting knowledge and experience will do this because concepts like separation of duties enforce this sort of thinking.