[sigh...]
If you begin teaching people about physics, do you immediately make them build particle accelerators or ask them to compute the orbital precession of Mercury? If they are only just beginning chemistry, do you talk to them about pi and sigma bonding in the amylase (sp?) structure?
No. You first teach them about basic definitions. Then you teach them about simple mechanics. Then you build that into Newtonian mechanics. Or you would tell them about the proton and the electron. Then you would teach them about orbitals (first the "2-8-8.." rule, then the "1s
2 2s
2 .." rule).
Now, at this stage, they don't believe you. So, you can build a catapult, and you can use your simplistic formulae to demonstrate exactly where the shot will land. And you can prove that the formulae work, by getting the aim perfect. The second example is harder, but theoretical chemistry is kind of well, theoretical.
Likewise, we show them what we predict will happen in a simple scenario, by using a simple scenario, to demonstrate the basic ideas. Later when they actually understand some of it, we move up the ranks of complexity. Your approach is like asking us to show Year 1 students QM, and then criticising us for not teaching them the truth. Well, maybe it isn't. But how the fuck can they understand the works of Shakespeare if they can't spell 'donkey'?!
Real scientists know there are a huge number of factors. And in their experiments, they document these factors and their effects, by first ensuring every other factor is perfectly the same and then changing the one they wish to test. None of these experiments could have viable, much less consistent or rational, results if they didn't account for all of those other factors. Guess what? The experiments work. Every time. So either some asshole deity is playing pranks, or they're dealing with those factors perfectly.