Sorry to sound like a politician, but there is not a direct yes and no answer to your questions.
Question 1
Yes your first attempt did not work because the images were in the wrong order.
But your conclusion is not correct.
The alpha over node places the second input over the first input.
So the top input is the “lower” layer (it is the image that will be underneath) and the bottom input is the “upper” layer (the image that will be on top).
I know it is a bit strange but this is Blender!
Question 2.
Sort of.
In the shader editor the “mix shader” and the “mix colour” nodes factor does NOT invert the effect.
It does the same thing as the factor of the alpha over node.
The factor slider for any node will always go from 0 (do nothing at all to the first input) to 1 (total influence of the second input)
So your last statement ( 0 = 0% and 1 = 100% applied ) is correct for both the “alpha over” and the “mix shader” nodes:
You might want to take a look at this thread that also talks about the alpha over node:
Edit:
Ha, ha, its the firs time someone called me that!
“The devil knows more because he is old than because he is the devil.”