The long-term plan for Rust is to treat its standard library (almost) like any other crate, so it could be recompiled with your custom compiler settings if necessary.

However, libstd is by necessity tied quite closely to the compiler, it's one of the oldest and most fundamental parts of the stack, and there are tons of little complications around making it "just" a crate, so changes to libstd/rustc/Cargo necessary to make that possible will take longer.

In the meantime, changing one problematic compiler flag seems like a sensible solution.