Baking, blasting, and chemical. Makes no difference. The core plugs have no affect of the result. Factory heads have core plugs in them and no one has ever removed those due to some concern.
I have never had a 427 block or any block with screw in plugs, so I can't even speak to how difficult they may be to remove after decades of having found a home where they are. On knock-out plugs, I remove those because I like to give the block an intense pressure wash in the jacket before I do anything with it and it helps to remove the plugs to get into all the crevices and flush out the silt and rust. A pro cleaning doesn't have this concern.