Is there a way to disable the automated underground workcarts entirely, or what is the convar to prevent them from spawning? I have the tunnel triggers set to false however they're still automated with conductors.

The following config options should not automate any underground workcarts.

"EnableTunnelTriggers": {
    "TrainStation": false,
    "BarricadeTunnel": false,
    "LootTunnel": false,
    "Intersection": false,
    "LargeIntersection": false,
    "VerticalIntersection": false
  },

Unless you have custom map-specific triggers which you placed underground for that map/seed, in which case you would just need to awt.remove or awt.disable them.

To troubleshoot, you should use awt.show in-game and go to the workcart spawn locations to see which types of triggers are down there if any.

If you previously had the workcarts automated underground, but then disabled them in the config, the data file may be remembering that those workcarts were automated and therefore is keeping them automated. To reset them, you can run aw.resetall.