Rust does let you communicate variance (it's very important for lifetimes). Variance is determined based on a type's composition, and PhantomData can be used to specify variance that doesn't immediately follow by providing an "example" of what it should behave like. The only limitation of this approach is that you can't override the compiler's reasoning -- if it sees evidence for covariance, and you provide more evidence for contravariance it will just give up and pick invariance (which is of course strictly correct if both pieces of evidence are accurate). Also I guess you can't have bivariance but like... bivariance is so bad.
All of Rust's standard collection and smaht pointer types are written in pure Rust and have relatively complex variance behaviour.