Is it possible to add a setting to choose the capacity of chests, otherwise it is impossible to play through cybersyn?

Why is it impossible?

Small capacity of chests, and if you play through a station = 1 resource, then it’s easier to make a railway network the old-fashioned way

Skill issue

Then make carriages with 5 capacity and it will be normal!

Barrels hold a lot, but chests hold almost nothing...where's the logic?)

That's true barrels need nerfed as well—their current state is a hold-over from pre 2.0 Factorio.

looks like I'll have to get into the code and make some normal chests for myself)

EI containers max size is 64—unwilling to compromise on the release defaults.

There is a method to the madness resulting in a desired level of difficulty.

Feel free to remove limiter in personal file, located in /scripts/data-final-updates/final-recipe-fixes.lua at the bottom.
Will be moved to /scripts/data-final-updates/items.lua in 1.1.97.

An alternative idea is to allow explicitly specified larger containers with enforced appropriately difficult recipes—see: EI logistic containers requiring simulation data.

Is it possible to add it to the mod settings so that users themselves can set the max size of chests?

Choose: Walk barefoot across—

Shattered glass

OR

Flaming hot coals