The Cargo.toml file changes rarely, and pretty much in an exclusively additive way. There hasn’t been any formal policy adopted about this, and its possible there will be small breaking changes in the future, but you should feel pretty comfortable about the stability of the format in my opinion.
There was a recent change in the TOML parser such that it accepts syntax that was previously not accepted. This new syntax is intended to be used by Cargo. Therefore it is possible that you’ll encounter issues. More details here Deployment timeline of cargo target-specific dependencies