One possibility is for rustc to take extern crate declarations as commandline args and for cargo to invoke them based on what's in the toml.

This technically already happens

Right, I guess there's no info needed outside what the --extern flag contains.

You have modules, use, extern, cargo.toml, cargo.lock. It looks quite verbose and redundant to me. I expected it to simplify but moving more to config files seems a backwards step. I may be biases but I find the Go import/packing vastly superior in terms of usuability(i.e using a single import statement you make the import explicit and ready to use). I think the trick is to build the tools on top of the source code not on top of config files(i.e ala C/C++).