There are certainly operational issues around centralized power vs decentralized engines attached to the train itself. If successful, the additional construction cost could easily balance the fuel cost of moving engines around with each train, and maybe additional maintenance required for a moving engine vs a stationary engine. It's probably worth comparing to electrified rail service, which shares the benefit of not shipping fuel with passengers.

In addition to all the safety constraints mentioned, it's just simpler to build a 12-inch diameter vacuum pipe than a 12-foot diameter pipe. It might be possible to constrain the rolling stock on a line so it all clears the pipe, with some trains propelled by the vacuum pipe, and others propelled by an attached locomotive (such as maintenance vehicles, or conventional trains when the vacuum system is under maintenance, etc)