Since lockdowns I think the underground only recovers around 70% of its operating costs. Maybe you have seen different figures?

The freezes eliminated investment projects needed to keep pace with population growth. There's also just big problems maintaining the stations and doing more than the bare minimum needed to keep the lights on. Travel on it and the stations are dirty, overly hot, etc.

Drivers on London's roads are very heavily taxed already, supposedly to reflect those externalities. Public transport obviously also contributes to pollution and congestion, especially when building underground lines, it's not externality-free.

I don't think TfL has a cost crisis. Crossrail overran but that was mostly due to the software complexities of the signalling tech debt around the Heathrow tunnels and other issues that can affect any kind of project. It's just hard to tell right now because they can't build at all.

The fare freeze was broken by central government briefly, but only by bribing Khan with central government money for upgrades. Exactly the outcome he wanted!