IIRC, and I could be wrong, factory heads had studs. These are removed when going to headers because 1st- installing them over studs is major hassle when also negotiating steering box, motor mounts, oil filters, k frames and drag links, and 2 - studs are long enough to cause interference with some tubes with a tight radius and this length will interfere with the tube to such a degree to prevent the flange from getting close enough to the face of the port to seal.
With that said, I have left studs in place and used them with headers, but they required some customization and this was only in a truck engine bay where I had a lot of room.