My opinion on turning the egr off and not blocking it is that it's a bad idea. If you turn it off it needs to be blocked. If egr is turned off but the flow of exhaust isn't blocked at the back of the egr cooler, the cooler won't last very long. Those hot exhaust gases are just trapped in the egr cooler, they have nowhere to escape to. At least with the valve functioning those gases can be somewhat cooler because it has a flow path. This is just my opinion on it so if i'm wrong and someone wants to correct me, I'm all ears.
If you have to pass emissions I don't know what to tell you. I personally would buy an 04 pipe that has no scoop, have it welded and then swap pipes once a year. Sounds like a pain in the ass but that's what I would do. Yes I know, Not everybody can do the work and nobody wants to shell out the $$ every year to have it done. It might sound stupid, silly and annoying but it would work.