I grew tired many years ago of folks telling me I had to have faith in order to understand why 3 year old children get ran over by trucks, or 13 year old girls get gang-raped, or why 100,000 people die in a storm...what the hell kind of "god" would allow that shit to happen? Really!
That has no bearing on whether a supernatural exists. However, you are not the first and you won't be the last person to raise that issue.
Some possible explanations.
1) There is no God.
2) There is a God but He only kick started things and then let nature take its course.
3) There is a God but there is no possibility that humans could even begin to understand a motive for His actions or lack of actions.
4) God does not exist but a god does exist. That removes all relationships with Bible etc. Who is to say a god has to be good? Hitler was not exactly the best fellow but no one denies he existed.
If God or a god exists then I think your scenarios are easily answered.
So we are back to the fundamental issue of.......is there a supernatural....
Both sides of the argument are based on faith. In my opinion the current state of science makes the science answer a greater leap in faith. There are couple of simple reason for this.
1) Science has given the show a beginning with the Big Bang and in addition has said all physics and time breaks down, does not exist, so science has bailed out.
2) The Big Bang is not true. If that turns out to be the case then it is just another case of science being wrong in this area.
For someone to 100% exclude the possibility of a supernatural is very illogical. One reason being that 100% excludes the possibility of life forms in the universe that are higher than man.
Someone did ask earlier in the thread about a definition of a supernatural. Well, compared to the small lizard or ant in the garden a man is a supernatural. All the ant's instinct's tell it there is no rain about but the man decides to water the garden

To say that man is the highest in the universe requires a huge leap in faith. But that is required if you 100% exclude a supernatural.
To take the analogy with the lizard one step further. The lizard knows the deal when it sees a mouse or a fly. The mouse and the fly also know the deal and because it has been repeated over and over through their lives. It is their "science" because it is predictable. They have been teaching it to their young for eons of time.
However, if the man sets a mouse trap then the mouse's mates are at total loss as to what happened to their mate. The lizard is equally confused with the loss of his prey. To confuse the issue one of the lizards also gets caught in one of the mouse traps. Yet the dealers in death are lifeless. They don't eat their prey. Impossible.
No matter how much experience the lizard and mice gain they will never be able to cover the man's next move. In other words their "science" will never cater for or predict what the man will do next and hence man is a supernatural.
Does anyone of this thread seriously believe that man is the highest form in the universe? That is what you need to believe to 100% exclude a supernatural from the equation.