> your 2 second gap is a pipe dream, not technically but logistically. You need scheduling flexibility to maintain such small gaps.
A 2 second gap means that a pod needs to sync and squeeze between two vehicles 4 seconds apart, or 45m at 40Km/h. That's three seconds of 0.3g on a 40m acceleration track, after which it can merge with no assistance from the other pods (in a practical system, they would clearly cooperate). Assuming you achieve 90% of full 2s capacity, a pod will wait an average of 20 seconds for it's slot - queues should not form outside of very busy stations, that would be connected to very thick pipes anyway.
> How do you avoid empty returns to the busy area?
You might need to return empty, you might not. There might be a triangular route available that can maintain fullness throughout. You could build a buffer in anticipation of the rush hour. The train absolutely needs to follow the same route back at the same time interval and there is no way to reallocate part of the return capacity to the forward, overloaded route by a simple lane direction reversal. (to clarify, I am talking about maximizing peak capacity at rush hour on a given overloaded segment, there would be significant empty runs during the rest of day like in any other system).
> At higher scales, one train tunnel is just enough at the terminus stations
That's because you only have underground trains to places where a full tunnel makes economic sense, so the city is substantially under-served.