That’s because of the WebAssembly type system: “Integers are not inherently signed or unsigned, their interpretation is determined by individual operations.”
Even though the System API uses i64 it will be interpreted as an unsigned number similar to how the existing ic0.time : () -> (timestamp : i64); does it.
It is also worth noting that the ic0.set_global_timer() will not be directly exposed by Rust CDK. Instead we will have a higher level library operates on proper time types.