So-it's not a bug, but an undocumented feature, eh?
Thanks for clarifying this - I've never noticed that "step" on the block and how it could foul an exhaust flange!

I see what you're saying.

Looks good:

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It's not bent out, the ports do line up (visually) there is more metal beneath the other port than the one on the left so it looks like it's bent way out. If you look beneath the port on the left of the first image, and imagine the same amount of steel there as the opposite side you can see that that entire corner will then foul with the shoulder of the block. Those flanges are quite deep, possibly too deep hence why the removal of that lower corner section also looks like they have cut across through the bridging bar.

Judging from the photo, since the cut flanges do not line up, the last port is a bit warped out of place.

That's not a problem, even new headers are often a bit out of line. Just bolt it to the head and apply heat until it lines up. Then mill it flat. A machine shop should know what to do.

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]):

Nice header! Is the flange broken at the aft exhaust port or is that the way they were built?

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