Because of how containers (chests) work right now, unlimited long chests are not really feasible as each one requires its own sprite. As eradicator points out, definitely possible, but not something I will be doing any time soon.
As for boxes in multiple dimensions, that could potentially be done, but it would require a lot of sprites (which I suck at making) and would take the mod in quite a different direction than what it was originally made for. I could instead recommend you mods like Angel's Warehouses or Ore Silos for those purposes.
I personally believe the inventory size for the chests is in a good place right now, but if you want to change it yourself feel free to do so. Chest sizes can be found in prototypes/entity/entities.lua, simply change the inventory_size to whatever you want.
I'm sorry I couldn't implement your ideas, but I appreciate the suggestions.