You assert this like it's a fact. But it seems like something that could be proven wrong. I don't see any real fundamental obstacles here.
You'd need to do some engineering obviously. But it's not a particularly hard problem. Don't crash into the thing in front of you if it hits the brakes for whatever reason. That about sums up the scope of the issue.
There's probably a bit of math involved that tells you the minimum safe distance where emergency braking can still work given a certain speed. If you get humans out of the loop (which the Boring company obviously has not yet done), it's basically a function of how quickly individual pods can react to each other. Which would be measured in nano seconds probably. You should be able to get a pretty decent throughput.
The nice thing with small cheap tunnels is that you don't have to squeeze everyone just through one of them because you can have more than one going all over the place. Most subway systems are a compromise on tunnel size where you basically end up with only a few of them because they are so expensive to build.
They are literal bottlenecks because lots of people end up being funneled through a handful of stations via a small number of tunnels. By the millions.
If you've ever tried to navigate the London underground during rush hour, it's not a pleasant experience. You basically have people shuffling back to back through tunnels and being crammed into railway carriages by the hundreds.
The premise of the Boring company is very simple: digging smaller tunnels at scale is going to have economies of scale associated that means you can have vastly more of them for the same money.
I agree their execution hasn't really delivered yet. But it still could. Probably waiting/hoping for FSD to solve the problem of routing wasn't the optimal move. But that doesn't invalidate the core premise. The tunnels they've dug aren't that expensive. So that part seems to be valid.