> like getting a dependency of something not written in rust, or picking features based on some system configuration

I've found that things like this are pretty straightforward with a build.rs and you aren't context switching between a configuration language and your target language since build.rs is just a Rust program that outputs configuration values via println.

> ... very complex applications

That's not always a feature for me, the amount of time it takes me to ramp into a complex CMake configuration vs arbitrary crate is significantly different since the conventions are well established. If you spend any time cross-compiling things the Rust experience(I.E. first-class triple support, cc crate) is miles above anything CMake provides.