In the factory, the cam shaft bearings are bored with the flat cylinder head surfaces as a reference plane. This results in a straight cam bearing bore when the surface is flat.
Unless the machine shop clamps the heads so that the cam bores are straight first and then decks the heads, you will end up with a deformed cam shaft axes. After installation, the cam shaft will now flex with each revolution and might eventually break. I've seen at least one example of that happening over at the 100 series forum. I would certainly ask your machine shop how they are insuring the straightness of the camshaft bores.
If the warpage is minimal the head bolts will probably straighten out the heads. The cam bores will then automatically line up again as well. That would be my choice. If badly warped, then new heads or used flat heads.