I think King Arthur has been outsourcing their milling for a long time, probably decades. I know they use several mills in Kansas, because PJ wrote a blog post about their taking several of their bakers and sales reps there each year to see where and how the wheat is grown, handled and milled. (Oh, to be part of one of those trips!)
During the worst of the flour shortages, they were buying flour from some mills they don't normally use, and there were reports of quality/consistency issues that may have been a result.
There's a lot of opinion in that article and not much of it backed with citations, it strikes me as the kind of article that could provoke a lot of passionate discussion.
I know that in France many bakeries have long-standing relationships with their mills, to the point where they know which farmers will be growing their wheat, what varieties, etc. The mills keep in touch with their customers about quality issues during the year, too.
That may happen in some US artisan bakeries with access to local millers and farmers, but most bakers, especially home bakers, have to deal with what we can get.
I've only bought a few bags of whole wheat flour in the roughly eight years since I got a Nutrimill, so I'm not the best judge of packaged whole wheat flour, but I will say that I noticed differences in dough texture and flavor when I started milling my own flour. (To start with, my whole meal breads are a touch sweeter.)
My mill is an impact mill, not a roller mill or stone mill, and there's not a lot of information out there on what an impact mill does to the wheat. I suspect there's a bit more starch damage than with flour from a commercial roller mill, I don't know if that'd be true for stone-ground flour as well. SOME starch damage is a good thing, because that's where the sugar comes from that the yeast feeds on, but too much starch damage is undesirable.
I can also notice a difference between flours made from winter hard red wheat and spring hard red wheat, though its hard to say exactly what. I've also used soft spring red wheat, in fact some of the best croissants I've ever made were made from some freshly ground soft spring red wheat. I've got some white wheat berries but have yet to grind them up and do any test bakes with them. (Some years back I bought a bag of white whole wheat flour, we were not impressed with it.)
The wheat breeder I know seems mostly concerned with things like yield and tolerance for drought, insects and plant diseases. I don't know how much he studies the nutritional aspects of his wheat tests, and it appears he doesn't know much about what happens at the mill. He also grows triticale, but interestingly enough the triticale breads I sent in to my wife's office last school year were the first time he'd actually tasted bread with triticale in it. (I doubt I'll be sending in any baked goods this school year.)
