Let's go over this again: Logic does not equal Science. Logic means that, with given settings within the story, things that happen make sense. If I read a Thriller that is about a bunch of people being locked in a cabin and tortured to death by a normal human being, that in itself is not our world. It may look and work the same as ours, but those people haven't existed and if they did, they likely didn't suffer the same fate, thus this didn't happen in our world, which makes it a fake account of a world that looks like ours, but isn't really. That is F I C T I O N.
If I now write a story in which I go to the lengths of building up a society that, in itself, explains why people have not widely heard of magic, yet magic does exist, it still makes sense. That it L O G I C.
I agree on the fact that, if you went deeply enough into the system and explained it so far, you know the origin of it, which I do in more than one of my stories, it could become sort of Science Fiction, because it ripples the boundaries between what is Fantasy and what is technically the Science of the world displayed. But in this one, I go more with the way it is portrayed, where a story like Star Wars, with so popularly called "Space Magic" in it, is still Science Fiction, while a story with explained Magic (like my own, as I mentioned) is still Fantasy, as it's set in a High Fantasy setting.
To get to your apparent conundrum, as
@TheBestofSome has gathered, which doesn't make sense to me at all, but we'll get to that:
@John_Owl got ahead of me in saying it, while I was typing.
I'm sorry if I come off rather pissed, but that's what I am, because a lot of people with a lot of influence have lately come to the same conclusions, which are simply a telltale sign of them being creatively bankrupt. Why would one more thing in the world, which may not be accessible to everyone in the first place, change the entire system? If it's big enough, and known to all, it might change little things, but not the major ones. In one of my more recent stories, I have incorporated Gods being there to protect worlds and taking Acolytes within them, giving them powers and even granting Miracles. There's one God whose Acolytes aren't even human anymore, judging Acolytes of other Gods if they use their Divine Powers to harm humans. And now? Nothing now, people know Gods exist, but they still function the same way. The world looks the same, maybe a bit less Global Warming, but not even that really. Magic exists in the daily life of humanity to a small degree, but that doesn't change how people live their lives. For example, there is a church that can heal, but they don't have unlimited people with healing abilities. So the general populace still relies on hospitals. In a system with healers as a choice, rather than being chosen (which is the case in my story) and thus rare, they would then gather up in houses, taking the places of hospitals and doctor's practices.
Why would it change much? When we didn't have electricity, people still sought sources of light. People lived the same way, no matter what they had. In a world with magic, there might be more things run by magic, but they will do the same things, because people need the same things. When movies didn't exist, people gathered in front of a Laterna Magica, in order to get to see something to amaze them and listen to stories. When we couldn't write, we drew on cave walls. Logic in stories largely depends on common sense, which we know from daily life. That is also why clichés work, becasue we know them and rely on them to understand things we aren't yet told, as they are mostly based in patterns we have seen before, and a lot of them are grounded in reality, polished and put into stories so many times we might have seen them ad nauseum. And if people don't widely know about magic, there won't be anything different at all, because, if not used, the energy used to actually DO magic isn't obvious to anyone, unless you write a story in which it takes a different form, then you will have to adjust the world slightly, so it makes sense again.
Again, Science is logical, but logic isn't Science. You don't need Science for things to make sense; you need RULES for things to make sense and as I said before, those don't even need to be figured out by a genius. People knew water was wet before they knew the word "Science". As to the the basic powers regulating the world: Just because magic exists that can make something float, it doesn't mean that everything floats at any given moment.
The world itself will work just the same, which is also why is makes "sense" for a story to incorporate the risks of using magic on a scale too large for the planet to handle without consequences. They usually can't even do that much, but in case there was a God, for example, or some super overpowered human / demonic / whatever character. Nothing just magics away the common elements of the world, unless the story states it. Grass is green, and unless the author describes it otherwise, we will assume the grass is still green, even when a character travels to another world. Someone using an additional energy that can be canalized into, for example, taking away gravity from a certain area or object for a certain amount of time, doesn't mean there is no more gravity.
Unless you somehow believe that "magic existing" means that every possible magic happens at any given moment, everywhere around the world, which would not only mean the worlds rules differ, but also every human is likely to be dead, I don't see why it would mean anything. If anything, it's what truly sets apart Fantasy from Sci-Fi, which creates a perfect arch back to my point earlier, because Fantasy and Science would hereby coexist, yet not go hand in hand.
Know the difference.
Also, I was rage typing here, so if you find unfinished sentences or a gazillion typos, you can keep them.
