The removed check was adding a protection for the case where a `Reference` has not yet got its reference count initialized and a script is called on it. That would cause the object to be released after the call. The removed code was constructing the `Variant` via the `Object` constructor so it didn't deal with the reference count and so the release was prevented.
However, `Variant` no longer works that way so that check was useless. Now it's just illegal to run GDScript on a Reference whose reference count has not been initialized.