It's called production tolerances. Have you ever tried building your own set of headers? You're welding thin wall tube to a relatively thin flange. It doesn't matter what kind of jig you use, there is always some amount of warpage.
There's more variation in some of those headers than I would like to see, and it's possible that Doug's has made changes to their production tolerances and are now sending out headers that have larger dimensional variances than they used to. Not sure. But if you understand the production of a set of headers, you'd understand that they're not going to all be identical no matter what. Profit margin tends to dictate what you accept and when you start tossing stuff in the recycle pile, but none of them are ever identical. The same is true for these cars. A 1/4" of body variation is commonplace. Header clearances on these cars often boil down to less than an 1/8". You see the problem. Adjustment is required.
We've been down that road several times in this thread. His motor mounts are no where near the stock dimensions. But although it's been pointed out many times, he's never posted anything to suggest he's tried anything different.