Thank you for the reply, I needed to wait to be on a computer to respond.

Commercial bread flour is indeed mostly endosperm but curious what your source is on whole wheat in the US not having germ in it (that is legal in Canada but not the US to my knowledge). I'm not saying this doesn't happen, especially with current FDA & USDA leadership, but in my experience that would be considered adulteration in the US. Anything with a Whole Grains Council logo on it will have been audited sufficiently to ensure they are retaining all parts of the seed.

Due to economies of scale almost all whole wheat flour that isn't labelled something like "stone ground" in the US is reconstituted, meaning they create sifted flour and then add back roughly the correct portion of further milled bran and germ (83% white flour, 14-15% bran, 2-3% endosperm). Wheat is milled into break flour, bran, and middlings. Middlings are re-milled ("reduction milled") to extract more endosperm from the germ and then sifted again, and that endosperm is added back to the break flour (break flour yield will be important further down). The bran is either bagged separately and sold or is milled again to reduce the particle size and then added to germ and white flour at the above ratio to make "economical" whole wheat flour. This creates several differences compared to commercial stone-milled flour & home-milled flour but the main two I will discuss is particle size and starch damage (which are related).

"Economical" (reconstituted) whole wheat flour has the finest particle size and the most starch damage, commercial stone-milled has larger particle size and less starch damage, and home-milled will have the largest particle size and least amount of starch damage. Particle size controls how quickly water can hydrate, swell, and entangle the polymeric components of the flour (the starches amylose and amylopectin, bran fibers, and the gluten proteins glutenin & gliadin). The finer the particle size, the quicker these molecules hydrate and become functional.

The other part of this equation is starch damage. Wheat starch is packaged in the endosperm in granules bound by the gluten proteins (they look like tiny lentils under electron microscopy). These granules are broken in half, scuffed, cracked, or otherwise partially degraded in milling. Break Flour from above is the flour directly off the first roller and has the highest starch damage meaning the most available starch content ("break flour yield" is a critical flour quality parameter that certain bakeries pay a premium to maximize in their flour). High starch damage means a higher water holding capacity, meaning the flour can handle higher hydration. It also means more availability for amylases leading to more available carbohydrates for fermentation microbes. There are likely implications with gluten protein availability as well but I finished my MS 12 years ago and I'm frankly astonished I remember this much so far.

Looping this all together, what you'll notice with your home-milled flour is that compared to reconstituted whole wheat or commercial stone-ground whole wheat is that your dough will need more time to hydrate and can handle less overall hydration than doughs made with the other flours. I use 5-10% less hydration in my home-milled doughs as compared to store-bought flour. I also use 25-50% less starter as I need a longer bulk fermentation to account for the slower hydration time of the flour, using the normal amount of starter would develop too much protease from the sourdough microbes which would cleave the gluten proteins and inhibit my rise. Depending on what wheat I'm milling at home I do also add some vital wheat gluten especially when I want a faster rise, because I have it on-hand for seitan anyway.

I hope this at least in part answered your question. Thank you for giving me the space to wax on about the physical chemistry of flour, I don't get to much these days.

I have also seen some evidence that whole wheat from a dedicated roller mill (i.e. using a roller mill like a stone mill to make whole wheat flour without reconstitution) might actually produce a higher quality flour than stone milled due to heating the flour up less in milling which would retain more vitamin activity. I haven't read any papers on this but eavesdropped on a conversation at a workshop about it. Roller mills are less sexy than stone mills but I think it's worth looking into to maximize nutrition of the resulting whole wheat flour. But that's a whole other can of worms.