I believe the yellow squishy nuts are a corn-based product. They are bio-degradable (for you GREEN fans) and melt into a glob if moisture gets into the package, then will eventually harden like a rock. Not a chemist, but I think there is nothing petroleum based in the "corn-nuts". They could eventually adhere to a painted surface of a train and lift the paint if not removed properly.
Bottom line is I agree, always wrap an item in tissue or other paper before bubble or other wrap. I use all the above, tissue, newsprint, foam wrap, bubble wrap, air pillows, different types of foam peanuts and corn nuts, even pieces of rigid foam, when I can get it. If these items are used properly, there will be no problem.
The last time I had an item damaged was when we were putting Fragile stickers on every box and shipping everything through the post office. I had 2 items, one was an AF Wide Gauge Electric loco, impaled by a sharp object, destroying the train. All my packing material and internal bracing plus double-boxing, could not prevent this. Our postmaster, at the time, told me employees in the sorting facilities resent seeing fragile stickers and tape and go out of their way to damage such items. Have had no damage since we stopped using Fragile stickers, also shipping 90+% through UPS now.