The tacit assumption of the OP is that it is better to do something else. That is, to start with some sort of first principles and create from scratch the artifacts that your project needs. It is telling that his example is a build artifact - these tend to change infrequently. The only way for one human mind to truly "dwell" in the space of project builds is to maintain many of them at once, as many as it takes to fill your days with nothing but build concerns.
"Tools that enable this pattern are harder to use securely..." Harder than what? A totally custom build? One made from first principles? I would, in fact, argue the exact opposite. And in fact I would argue that copy-paste-modify serves practicioners very well, especially when it comes to on-boarding. If you disagree, do the gedankenexperiment where you imagine joining a team with a totally custom build versus one with a lightly edited common make file. Which experience would you prefer, all else being equal?