beantwin,
Firstly you are not the first person to ponder these questions. You should begin with some good introductory text on QM which discuss this.
Two phrases in your OP which I note are "...and we cannot model with certainty..." and your last sentence "Please... ,but instead grounded in reality."
Firstly a model is a construction which we either observe or hope to observe matches the behavior of some actual physical system.
Secondly, my thesis advisor taught us (his students) to make a distinction between reality (what is) and actuality (what happens).
Understand that via the empirical nature of science what happens (in the lab or observatory) is more fundamental as a source of knowledge and truth that what is which we can sometimes infer from the former. Jazzy or not, this is the more proper way of looking at things. Science studies how things behave and sometimes can construct a "model of reality" to fit that behavior. This connects with our day to day experience of updating our world picture with our experiences.
But this begs some questions:
1.) "Is our world picture correct? or is there another or many world pictures which equally match our experiences just as well?"
and the deeper question:
2.) "Is a reality model appropriate to the phenomena we observe or should we in science stick to describing and explaining phenomena in terms of their relationships to other phenomena?"
I have found that in order to better understand quantum theory, it is important to explicitly distinguish questions and assertions about the reality of physical systems from the questions and assertions about their actuality.
In your example of atomic orbitals, quantum theory does an exceptionally good job of describing behavior (the actuality) precisely and accurately. Your questions beg for an understanding of "the reality" as if there must be one. Consider the possibility that anyone "reality" is not going to fit all actual behavior, that reality is relative.
Finally compare this antithesis of intuition with the similar one of relativity of time in Einstein's theory wherein two observers may meet at an instant and yet have very different pictures of "what's happening right now". One's future may overlap the other's past for spatially distant events. (This is not directly related but is another exercise in learning to make explicit and modify what one intuitively believes is "obvious".)