Any thoughts?

Yes, for the ex manifold bolts, penetrating oil applied often over a period of time. You should have already started that. Then heat, and lots of it. The nuts may come off or the studs may unscrew from the head. Either is fine as long as they don't break.

I'm not a machinist so I might be wrong. I was thinking you could remove the cam, put the valve cover on and stuff the hole where the cam was to keep chips out, and plane the head with the valves in. But, if that is possible, you need to do a compression test or cylinder leakage test before removing the head or t-belt to know if the valves are leaking. That test isn't valid if the gasket is blown between two cylinders, in which case you can remove the head, turn it upside down, and fill the combustion chambers with thin fluid like kerosene (gasoline if you are careful) and see if it leaks. Also, you don't know if the head needs to be planed until you get it off.

If the machine shop is removing the valves to plane the head, I would have expected that they would be doing a valve job, not just removing and installing. There is an added complication if you have stelite exhaust valves because I don't think they can be ground so if hand lapping won't correct them I think you have to replace them. You could need valve guides too. I don't think you ever said how many miles are on the car. Is that an unknown?

Charley