Yes, but no discussion of how you'd bring the system down if one broke down mid-trip or how you'd bring it back up. The individual cars only carry power to maintain speed, no to accelerate, so if they have to stop because something goes wrong, a whole bunch of people are stuck in the middle of nowhere without a toilet (or air?)

There's some discussion on pages 52-54 of the PDF.

I stand corrected. In fact it comes down to two paragraphs and doesn't really cover much including, for example, just how long this would take (the cars behind the stalled vehicle would use emergency brakes then proceed at low speed on wheels to the nearest station -- sounds like at least half a day of down time).

Yes but they need to be 5 miles apart so they would board approximately every 30 seconds and carry 28 people each.

Yes, a pod would depart every 2 minutes or less, which puts about 23 miles between them.

I think it's actually more useful to think in terms of "2 minutes between them", as opposed to "23 miles".

2 minutes is all you have - to detect the situation, make a decision, then stop.

How much time do you have in heavy freeway traffic?

Four seconds, if you're driving the way you were instructed. But you've got multiple options: go left or right, and if you slam the brakes they'll stop you in time. If something broke the tube, are we looking at several pods slamming into the obstruction one after the other?

The two situations you're comparing are vastly dissimilar.