I know very little about the cooling system on these engines. I have had a lot of experience working on Fords and other OEM vehicles and it is suspicious to me that the factory would go to the trouble and expense to install plugs in the heads and the block to purposely block these passages. That probably required 15 minutes of someone's time on the assembly line, extra inventory and expense of all those plugs. If they can save a dollar on each vehicle, that adds up.
So I bet there is a reason they are plugged. It may be something stupid like making the engine run hotter to help emissions, I don't know.
Sometimes I do these "mods" and find out what the reason was afterward. Like why they spent all that money for that complicated dual mass flywheel. No way would Ford be able to sell these trucks with them making all that noise at idle. And like the soup bowl mod. That seemed like a no brainer at the time when I read about it, and did it. But then people do not seem to comment or I guess they don't notice the constant low frequency drone from the intake when you are running at speed down the highway. It can get tiresome, though maybe some of you don't notice because you have a loud exhaust system.