They use an electric train to move the waste away underground. This comes with many benefits - including eliminating the need to drill ventilation shafts for workers (which cost time and money).
If you're not receiving federal funding for the project, the cost is pretty important. The Boring Company can likely do things cheaper than anyone else.
Raw drilling speed isn't the only area where innovation is occurring. I'm not sure if their biggest optimization (cross-section area) applies here, because the type of vehicles in the tunnels is a factor in that vision.