Hypotheses make predictions. Experimentation can test those predictions without providing an alternative explanation for the phenomena you are testing.
For example, if I came up with a theory of gravity that implied everything should fall towards the earth at the same speed, all you need to do to falsify my theory is show that this is not the case. You do not need to know that wind resistance is the confounding variable to know that the theory which suggests everything should fall at the same speed is wrong.
Again, you can’t make an experiment without an underlying theory.
I understand some concepts are so ingrained, that they are perceived as theories but as reality itself (Newtonian physics before the end of XIX century) but physics is not constrained by our intuition (what we are familiar with).
Could you provide an example? Because I did so, and you repeating exactly what you said earlier doesn't really invalidate mine. As far as I can tell, my example is valid and invalidates your theory that you need a theory to falsify another theory.
Let me try another example: you claim that anyone who drinks a cup of X liquid will die. I drink your cup of liquid, and do not die. I have falsified your theory. I do not know why I did not die, I do not assume anything about why I did not die – I just didn't die. Theory falsified, no alternative theory proposed.
With regard to dark matter: yes there are many competing / mutually exclusive theories surrounding it, but that does not then mean in order to invalidate one of those theories you need to have picked a different one that you like better.
Your examples assume the absolute and complete knowledge. It is not our world. There is no theory of everything (yet or ever).
If I would try to find and explain alternative hypotheses for your "human intuition/everyday experience " examples they would sound contrived this invalidating themselves. Imagine trying to explain quantum theory/general relativity to a Victorian and their counter-examples all use objects from their life.
Hypotheses make predictions. Experimentation can test those predictions without providing an alternative explanation for the phenomena you are testing.
For example, if I came up with a theory of gravity that implied everything should fall towards the earth at the same speed, all you need to do to falsify my theory is show that this is not the case. You do not need to know that wind resistance is the confounding variable to know that the theory which suggests everything should fall at the same speed is wrong.