As much as I agree that Rust needs a better story for builds and interacting with other languages, it sounds like you have a misunderstanding over what Cargo primarily does and what crates are. A crate is a single compilation unit of Rust. Cargo is a tool for compiling crates and pulling in other crates that it references.
build.rs is a half measure to include foreign symbols in compilation artifacts like static/shared libraries and executables. I'd go so far as to advise against using it for anything but specifying linker flags.
I don't think I've ever had a use case for specifying dependency versions at build time. That seems insane, and I do insane things in cmake with regularity. There's a reason versions are pinned to a config file committed to repos in almost every contemporary language.
fwiw, Cargo is a crate itself and you can use it as a library. You can even compile it with C language bindings to call through FFI in other build systems if you felt like it. The lang tools team has done a great job with keeping the scope of Cargo manageable and putting in the ground work to make better tooling around it.
For complex Rust builds, check out cargo-make. It does most of what you'd need in a predominantly Rust codebase. For polyglot environments, cmake with custom targets is the least bad way I've found to do it - and it's not hard to do that by shelling out to Cargo.