Yeah, and they stick down into the plenum quite a bit and there's next to no room just below them, especially on the side where the runner top covers most of the hole.
If you remove them, there's an ugly ridge in the top plate, the guy that bought my manifold (the one above) radiused the entire hole. I wanted to do that but was too lazy (even though I posted a small article about it on the cfi site back then LOL)