I'm thinking sloppy weld repair of previous foreign object damage, harder to see because the high spots have been milled.
...Is that another from 1:00 on #4 intake to the bottom of the prechamber?
Yes and it would be a bad idea for repairing cracks. High deposition and low pen.
What kind of tooling does one use to hold a head in place on a milling machine? It isn't as simple as just clamping it in a vice is it? What surface do you square up to when you have a semi-warped head, or a welded face?