I get what you're saying. But I've adapted my thinking over the years. I'll try to put it as succinctly as I can get it since this sort of topic can obviously take up far more than a comment on a forum.
I view religion as a tool. And as with any tool it can be used for good or bad. Also, whether or not we decide to keep the tool in our toolbox depends on one general question - "does it serve a purpose?" If the answer to that is yes, then it is a valuable tool. That is how I choose to view religion.
I also think many of the "supernatural" elements you mention are not to be taken literally. However, I do think it is important for human beings to believe in something other/greater than themselves. I think it keeps us grounded and more connected to reality rather than just viewing our existence as some sort of meaningless accident.
Most of the other supernatural elements have to do with a fundamental structure of the world and the way we view it. Meaning that they are stories that have been condensed down over time to explain some base value - i.e. the tower of Babel, the flood / Noah's ark, the story of Job. These are effectively parables meant to illustrate a key facet of life. They are equivalent to short story fiction designed to explain a component of a larger value system.
That being said, I think religion in general is usually taught very poorly to young children. I know it's hard to explain some of the deeper meanings to children but at the same time, if you talk to a lot of the openly religious adults they also don't seem to understand a lot of this. I saw some psychology professor talking about this problem, and he said that his guess to explain this would be that these stories have been so boiled down to their core components after thousands of years that they have become extremely condensed such that it becomes almost like a form of subliminal messaging. Not in the literal sense, but rather that these stories are so foundational that they are simply accepted as core truths. And because of that they haven't been challenged for hundreds or thousands of years. And because of that, people haven't had to put forth a proper explanation for them. I'm not saying they are wrong to challenge them. Or that the teachings are wrong. I'm saying instead that because they've had this sort of untouchable truth to them, people are just told "this is how it is" more or less, and no one has really been properly explaining why those stories are the way they are.
For example, there are many atheists that claim we can finally just dispense with the absurdity of religion now that society has basically become enlightened with all these fundamental human rights, lower crime rates, mass education, etc. They claim that society finally "gets it" for most of the critical stuff and human beings are hard-wired as more or less "good" and religion has only stood in the way over the millennia. But that's only half true. Religion has been misused, sure. But the problem is that even though human beings are somewhat a blank slate but also somewhat hard-wired for basic good (babies have been tested and shown indications of not liking violence, injustice, etc.), this doesn't mean there aren't other forces that aren't religious that may slip in and do the evil work of "bad" religion when it is missing. It's also not counting the fact many of the things those atheists take as givens are not, in fact, givens in much of the world. Take freedom of speech. They say this is obvious and would be granted for all if not for oppressive things like religion. But freedom of speech isn't the state of being for many, many parts of the world. They discount just how much the very fabric of western society is linked to the judeo/christian religions. The entirely of society is founded upon those beliefs. So if you think you can easily just separate the two by getting rid of religion, I think it is a way oversimplifying things.
Hopefully this rant made some sort of sense.