What's the difference?

Correct me if I'm wrong but... the EGR ports in the heads... might also be considered the passage that flows exhaust gas under the carb pad to heat the intake. You could weld this shut in the heads.. or the intake..probably a bad idea in a cold climate. My 340 had them carboned shut and even after being cleaned out I never noticed a difference. If the intake has the EGR valve or the block off plate bolted to it and the gasket goes bad.. man will you hear it! Then it vents exhaust gas under your hood! Don't ask me how I know... LOL!

Now if he means in the intake....... and I think he does... he's talking about the "floor jets" in the floor of the manifold itself. Easy enough to pipe plug these, put a little Devcon or similar permanent type epoxy in them, and smooth them off once it's hardened.
Some intakes have the pad for these jets cast into them but not drilled .

Attached pic has the exhaust crossover circled... most of the aftermarket performance oriented heads don't even have one.