I take your point for long-distance travel, but the same argument doesn't really make sense to me in the commuter context. if something goes wrong with the second leg of my commute, I probably want to figure out a different way to get to work, not turn around and go home. either way, I'd just end up taking a taxi, bus, or both. as long as it doesn't happen often, it's not a big deal.

personally, I am primarily optimizing my commute for low average travel time and variance. I'll always pick the fastest option that allows me to walk out of my door at the same time every day and get to work on time for >90% of trips. practically, that equates to planning transit where the second leg has very short headways, regardless of where the transfer happens.