I had to zoom in on a few pics to see the problem. I needed to remove the copper shims to see the problem. But maybe it works as there is a taper to the mating surface on the head and if you use three copper head shims, it may allow the head to tighten up against the copper head shims OK.
But in anycase I see your point, the head would not be able to tighten down against the cylinder and or shims without a recessed part where the threads are removed. I'll have to break out my lathe and do bit of relieving work there on my example too.
I don't really like the tapered part for the mating surface either, I think it ought to be flat, like the rim on the glow plug inserts as well. That allows for more surface area on the two mating surfaces to make contact and prevent leaks or seepage.