Large scale systems tend to fail. large centralised and centrally managed systems with big budgets and large numbers of people who need to coordinate, lots of people with an interest in the project pushing and lobbying for different things.
Multiple smaller systems is usually a better approach, where possible. Not possible for things like transport infrastructure, but often possible for software.
It depends what you define as a system. Arguably a lot of transport infrastructure is a bunch of small systems linked with well-understood interfaces (e.g. everyone agrees on the gauge of rail that's going to be installed and the voltage in the wires).
Consider how construction works in practice. There are hundreds or thousands of workers working on different parts of the overall project and each of them makes small decisions as part of their work to achieve the goal. For example, the electrical wiring of a single train station is its own self-contained system. It's necessary for the station to work, but it doesn't really depend on how the electrical system is installed in the next station in the line. The electricians installing the wiring make a bunch of tiny decisions about how and where the wires are run that are beyond the ability of someone to specify centrally - but thanks to well known best practices and standards, everything works when hooked up together.
Its when you need to coordinate it lots of bits. if you can modularise it its fine. If you have lots of small parts your replicate repeatedly its fine. So Each station is separate, they you lots of common components, trains come off a production line etc.
However building a single complex system as one project is the problem. A long distance railway line, especially if going through populated areas or difficult terrain that imposes constraints, for example.