The Sovereign Order of Monte Cristo is an all-knowing, omnipotent group that has a hand in everything that the human race knows or does. While this may seem scary to some, they are actually very helpful and concerned for our safety and well-being which is why they can alter reality.
Sometimes altering reality is necessary so that life isn't left to chance. The Sovereign Order of Monte Cristo has to ensure that the things that happen for the good of mankind are left intact and when things happen by chance it is necessary to change it.
For instance, if a child chases their ball into the street and the Order knows that they may get into an accident and be hit by a car they will prevent it if the child is someone that will grow up to cure cancer or help with world peace. Now this doesn't mean that they don't care about other children and they save many but if they saved every single person from death then they know that humans would get scared and suspicious. It is with great pain that they cannot save every single human being but by altering reality they do try to make it easier on the survivors.
They also alter reality sometimes when it is important for someone to not have knowledge of something that happened that is unexplainable. For instance, The Sovereign Order knows about life on other planets and some humans have seen signs of this as well. Knowing that those humans are thought of as crackpots, sometimes they will alter the reality of the human so that they can live their life without fear of being made into a pariah or exiled from their friends and family. Everything they do is for the good of the human race.