I feel like this is less a question about how to design an air-proof bottle and more a question about how to prevent the spoilage of a substance. We might need to think outside the metal container to get an answer. The first question I would ask is what in the air is causing the substances to degrade. It seems likely that the answer is oxygen, as it is reactive and makes up 21% of the Earth’s atmosphere. Water vapor is another possibility, but one that is disproven due to the substances being used in potions which likely contain water. Nitrogen is unlikely as it is not very reactive but does make up 78% of the atmosphere. The same goes for CO2, although it does react to water and form carbonic acid, but CO2 makes up less than 0.1% of the atmosphere.
To my mind, that means the method of preventing spoilage needs to be the removal of oxygen from contact with the substances. Before getting into solutions, we need to determine what is happening when air (or oxygen) encounters the magical substances. If we assume that the substances follow the laws of physics (matter cannot be created nor destroyed, merely change states) the oxygen would bind to the atoms/molecules of the substances and change them into a mundane/magically neutral form. A tightly sealed container nearly full of magical substance would thus have some portion of its contents spoiled, but the spoilage would stop once the available oxygen was bound into the new form. The spoilage is obviously not strictly from evaporation, as a container with vacuum space would not prevent evaporation and evaporation stops when external atmospheric pressure equalizes with emission pressure.
If oxygen exposure is the culprit, it can be removed a variety of ways, especially with 1998+ technology. The oxygen can be replaced with an alternative, such as nitrogen or a noble gas, prior to the container being sealed. Dropping a pellet of dry ice into the container would eject most, if not all, of the oxygen inside a container as it evaporated. An oxygen absorbing agent can be used to remove trapped gases. Something akin to ascorbic acid coating the underside of the lid which binds the free oxygen and prevents it from spoiling the substances. Vacuum sealing can also be accomplished using both rigid walled and flexible walled containers. The vacuum might not be perfect, but it would limit the amount of oxygen available. If combined with a flexible plastic or rubber coating, the substances would be well protected. This is used in food preparation to prevent spoilage. Put the substances in a metal foil sleave, remove the air, seal, and you are good to go. A well-designed system could even be used to re-seal opened packages after removing a portion of the contents.
It might also work to change the way the substances react to air to avoid needing such a container. If the substances are liquid, perhaps they form a “skin” when exposed to air. The hardened skin is of no use, but the liquid underneath is still viable. Or, as mentioned above, they degrade until the available oxygen is used up. Perhaps an additive can be used to extend the shelf life of the substances, but it causes an unpleasant aftertaste or makes the substance less effective and thus resulting potions are in less demand and sold cheaper. This would introduce an element of class division, as the wealthy could afford the better tasting/more effective potions, while the poor would use the cheaper mass-produced potions. Homebrew potions might become a thriving industry if people are able to create and use the substances before they degrade to make small batches.
If the substances are heavier and do not mix with water (think of oil and water, but the water on top), you could have a container with a spigot at the bottom and a layer of water on top. The spigot allows for the removal of the magical substance as needed, without risking the remaining liquid. Eventually, the container would have a small amount of magical liquid sitting below the spigot opening, but it could be combined with another container with little loss and excess water skimmed off the top.
The workers producing the substances might work in a chemically “clean” room, wearing breathing masks while working in a pure nitrogen atmosphere. If nitrogen was being forced into a room from above, and vents carried any escaping oxygen and CO2 away in floor vents, the substances would only be exposed to nitrogen. A lid with an inflatable bladder could then be used to pump out the substance as needed without introducing external oxygen into the mix. Think of a chemical spray tank with a manual pump on top. The bladder pushes the substance out a hose while preventing oxygen from contaminating the remaining stock.
The solution to the problem depends heavily on the story and if these substances “need” such complicated containers for the story to be told properly. If there is not a story need, focusing too heavily on a solution can be a waste of time. Handwave a solution and move on with the story. If there is a story need, then looking at the long history of food preservation might help. Push comes to shove; you could always just set the magical substance creation in space and import sealed containers which were never exposed to an atmosphere. Or you could just have vacuum pump technology advance rapidly and become mass-produced. Everyone has a vacuum pump to remove the air from substance containers and prevent their loss. A national standard could specify connector types and container requirements.
Whatever option you choose, it should fit into your story and make sense. There is no point in inventing new technology if readers will look at it and wonder why your world did not just use an obvious real-world solution to the same problem.