I don't know what the tube is for. That engine is the way it's dressed out in the Camaro. I only used the block, heads and oil pan and transferred everything else from my 2.8 onto it. It now looks lika a stock Fiero V6, sitting in my 87. There are several versions of that EGR. Some have covers encasing them.
This engine sat in a wrecked car for about 3 or 4 months before I bought it, so the flywheel probably accumulated a little rust, but generally, they are rusty in the areas you see.