There is a slight shoulder on the block where that part of the flange would/might(?) have fouled upon had they not ground that section out. Some fabricators leave it so that the fitter can grind off what they want. In this instance I'd say it was a slight design flaw (nice headers nonetheless) but provided the sit flush it should be fine.

If you look at some other flanges you'll see some are thinner (in depth not thickness) around that area to accommodate for that slight shoulder on the block. How much the flange will foul with that shoulder also depends on head gasket and how much the head and or block has been surface milled.

Image of the small shoulder/shelf that protrudes (located above the hole for the crankcase ventilation tube, quite close to the deck of the block [top right corner of the block]):