A lot of the laws of physics I’ve studied, like Boyle’s Law and Charles’ Law, describe the behavior of “An ideal confined gas.”
I’ve had to tell several flight students to unlearn what they’ve learned about that in the meteorology chapter, because, for example, in a confined gas, increasing the temperature causes an increase in pressure while the density stays the same. In the Earth’s atmosphere, increasing temperature does nothing to the pressure and decreases the density. Because the Earth’s atmosphere isn’t “confined,” there’s no lid, the air is relatively free to change volume. Heat the entire planet up and the atmosphere will just get a little taller.
But, I think, even if we put a magical vacuum tight shell around the planet 200 miles up, making the volume finite, I think the atmosphere would still act like an unconfined gas, because 1. it’s so vast that it never homogenizes, parcels of different temperatures, pressures and moisture content take days to slosh across the available space, and 2. the Earth’s gravity will cause a pressure gradient; most of the air is at the bottom and if you heat it up, it may not change volume but the pressure at the top will increase.
So I guess there has to be an upper limit to the volume and/or mass of air that can be “confined” and it’s somewhere below planetary scale.
There are what are called 1st and 2nd order effects. Gravity is first order. The sloshing is second order. So as you say, scaling the model up does make additional factors matter relative to your 1 liter of gas on the table. But it’s only the first order effects which make an appreciable difference when looking at it on a planetary scale.
Then if you say want to extend the model to your meteorogical model, you have to say, well… the density of air is different over the ocean because of evaporation. The gulf stream moves clouds consistently this way etc. But those things only matter after you’ve introduced gravity, and understood the earth’s atmosphere as the “gravitational balloon” model. Then you introduce your sloshing to understand the next stage.
This way of thinking about things in terms of leading or second leading order effects when considering systems at varied scales is pretty common in physics.
Btw from lived experience I can tell you the only gulf between you and a 150 level physics class is that you are actually trying to learn it.