I'm guessing you're looking at an aftermarket intake manifold and discovered it hits the top of the separator. I'd run into that at least a couple times.

Otherwise you set it aside when you disassembled the engine and now can't find it. Done that too.

The down draft tubes don't pull the kind of vacuum a PCV valve will on a healthy engine. Early ones used to have a rubber grommet that fit where the downdraft tube hooked up, had a right angle fitting in it which would hook up to a PCV valve using rubber hose.

I was always concerned about pulling oil out of the valley, so would put a frost plug in the hole mentioned above. Remove the separator. Use aftermarket valve covers with the PCV hookup, but make sure there's a baffle on the inside of the valve cover. Some of the cheap ones don't, and I've had trouble with them allowing oil mist to be drawn out of the valve cover.

Hope this helps.