Strength of a package is related to the strength of the packaging material and also the design of the package.

There are some fairly straight forward concepts to keep in mind when designing a lighting system: 

Oxygen levels below 1% are very effective in delaying rancidity, staleness, and other deterioration symptoms of pistachios and other tree nuts.

Since most gas diffusion is through the stem scar of tomatoes, you can modify tomato ripening by blocking the stem scar with wax and therefore you should consider this in any waxing treatment

I suggest keeping them cold and dry.  Therefore forced air cooling in clamshells or boxes should work fine and would be preferable to plastic bags.  If you use plastic bags, I would

Most researchers measure respiration rate as carbon dioxide production rather than oxygen consumption because the former is easier to determine.

The 40 x 30 cm footprint box is compatible only in that it is exactly half the size of the 60 x 40 cm box.  Some box designs have stacking tabs and other features to interlock the boxes.