Mutations are like skills that add to the profile. So if you e.g. suffer -1 Movement, then this is always added to your normal Movement. So your profile reads 4 and you subtract -1.
This is also the case with Serious Injuries. If you suffer -1 Toughness permanently, then this does not affect your profile - it is added on top. So you cannot make up for these modifiers by stat increases through experience.