Consider an example:

namespace Shapes {
  export namespace Polygons {
    export var S = 5;
  }
}

import polygons = Shapes.Polygons;

console.log(polygons.S); // 5

polygons.S = 123;

console.log(polygons.S); // 123
console.log(Shapes.Polygons.S); // 123

According to

Importantly, for values, import is a distinct reference from the original symbol, so changes to an aliased var will not be reflected in the original variable.

the S shouldn't be changed in this example, right? But it changes.

I'm not sure what "distinct reference" means exactly here. Maybe I just misinterpret this clause. Or maybe something changed in TS and it's not true anymore. Anyhow, its meaning isn't very clear.

It's also impossible to reassign an alias. Was it possible in the far past? If it is, then maybe this clause alludes to such a scenario.