a question regarding manufacturing

Hey, if she really wants natural, there's always BRIO.

Any plastics used on models need oil and all the associated refining.  Paints require chemicals and metals are going to need whatever industrial process needed to make the particular metal or alloy.

Rusty

There is no such thing as an "organic" train.

Might be able to grow a chia Pet and trim it up that looks like a train engine

Don't drink too much of the koolaid

While I claim no expertise, you could tell your wife the "smoke" produced on your layout pales in comparison to the contributions of the die casting and injection molding processes to China's daunting environmental issues, much less the oil drilling and metal mining to obtain the raw materials.  But I wouldn't do that.  I would just turn off the "smoke" and tell her she's the best thing that ever happened to you if she again brings up the subject of the material components of your trains.