What I am skeptical about is putting large car batteries in tunnels, which store enormous amounts of energy that could potentially be released in combustion and need be managed by adequate ventilation and fire suppression systems.

Versus an electric train. Theoretically, since the energy is transported into the tunnel via power lines, wouldn’t fire suppression and ventilation systems be cheaper since they wouldn’t need to handle so much stored energy potential (via batteries) traveling through a tunnel?

Yes, seems like it. An engineer acquaintance who builds subway tunnels says that they put in emergency exits every X feet, so that emergency-exiting people never have to walk more than a certain distance before they have a chance to make it to ground level. And in the case of an emergency, massive ventilation fans kick in (that are otherwise dormant). So, from what he's told me, the costs are less in suppression than in providing safe exit opportunities.