We discussed this in the Cargo meeting today. We agree with this proposal and analysis, and we'd like to see the 
settings added to Cargo.toml.
(This includes aliases, with the caveat that we're still discussing the handling of aliases that would conflict with built-in commands.)
If people send PRs based on this thread, adding related groups of config settings (not all of them at once), including corresponding documentation updates to the Cargo manifest documentation, we'd be happy to merge them.
We look forward to seeing these added to Cargo.