The L train is actually fully self-driving and self-operating. The TWU has a contract with the MTA that requires them to hire someone to sit around and press a keepalive button every so often, though that doesn't make the train any less autonomous.

(The TWU has a history of striking these sorts of "deals" with the MTA - typically, they take the form of requiring the MTA to pay for the cost of any jobs that are eliminated due to technological advancements. In other words, it becomes more expensive for the MTA to introduce technology - even technology that's already been standard practice for decades elsewhere in the world - than to keep using older and more expensive systems.)

So at this point, we're talking about political barriers to self-driving trains, rather than technological ones, and "repurposing subways for self-driving car tunnels" has all of those same barriers, on top of being a dramatically less efficient way of moving people around.