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I haven't really played much C:S1. You want to coose exactly what product will be used, so one zone per product? Detecing the environment isn't really possible with assets. If you want a all buildings to be copied to a zone for each resource, it will take ages to load, because there will be thousands of extra assets, just so you know.
In C:S1 you zone 5 types of industry zones: Forestry, Agricultural, Oil, Ore and Generic. As the name indicates the special zones deal with only those resource types, extracting or processing. Generic area then uses the end products from these 4 specialized zones creating goods that then will be sold at commercial zones.

What would be nice is to be able to zone similar zones, so for example forestry zone spawns only buildings that store or process lumber & timber. This way when I build a special industry I could zone this type of industry area next to it so that the resources provided by this special industry building are used right next to it.

I think this is what the other mod tries to do too. But ideally there would still be a division between clean and dirty types. So in essence, 8 new zoning types.

Agricultural processing / storage with clean processing
Oil - / -
Ore - / -
Forestry - / -

Then of course the vanilla type would be the ninth option for general areas.

Some industries use 2 types of input so in these cases it would be a bit tricky to decide which area that factory belongs to, so it could appear on both for example.

Hopefully this makes it more clear now.
 
You don't, that's part of the simulation. From my experience you need only a few warehouses at all times, so huge warehouse zones are hard to make without them being empty.
Also, every cargo port or cargo train station includes warehouse space built-in. Ordinarily, a port would generate a lot of warehouse development nearby to transload cargo both being imported and exported, but the inclusion of so much storage inhibits spawning of commercial warehouses.

There are 2 ways I see to induce warehouses to spawn.

1. Do not build ports or cargo train stations (and if you do, certainly do not add the warehouse upgrades!) Instead, build extra connections to outside edges of the map- connect as many highways and local roads to the edge as you can. This will allow import via trucks which may need to be stored.
2. Build as many specialized industrial areas as you can fit- farms, trees, ore, oil, stone, and coal all will require warehouses if you produce a lot.

Remember to also build regular vanilla industry as well, because they process your raw materials into products to be sold in your commercial and offices as well as for higher value exports.