They used large diameter boring machines for some of the lines, which allowed for putting opposite directions on top of each other, rather than the standard next to each other configuration.
So at a junction, you would have four tracks inside of one tube, and the other line be right across when the train stops. Now they sync the two different lines to always arrive simultaneously. Thus a transfer is you go out of one train, and right there, across is your connecting train.
I’m not sure how much the whole thing cost to implement and maintain, but I do think it was all worth it. It allowed them to have really accurate and fast travel times across all the lines connected this way.