You are right if you take a container initially filled with gas at 1 atm. Then when you open the container to the earth atmosphere, you get an equilibrium situation (although not exact).
There are other thermodynamic factors that has to be considered - Temperature and Entropy.
Equilibrium is defined to be when none of these quantities change with time, more precisely when the average fluctuations are zero.
Henceforth, its pretty easy to see why two different systems having equal pressure ONLY need to be in "equilibrium".
To answer your question, any two system need not be in isobaric equilibrium always. Consider your case, here you have two systems,
- The container
Now, you usually don't have control over the atmosphere, but you will usually have full control over the container, in the sense that you can fiddle around with the various thermodynamic quantities like Temperature and Pressure. Suppose you fill the container with idea gas, then it satisfies the relation $PV=NRT$, where you have two independent variables. So to get pressure, P > 1 atm, you could in principle change the volume of container(take a different container) and its temperature so that you get P > 1 atm.