pure speculation... but there are certain food that need to be pure-- (the flat bread used as eucharist) some mill would be set up with 2 or more sets of grindstones (grinstens)and could seperately grind two different grains.. but small mills would only have one set, and would grind wheat, till it ran out, and then grind corn.. and between the two "runs" there would be corn flour, contanimated with some bits of wheat. (this would be run of mill.. ) flour for special food would not be run of the mill...

secondly, as a farmer, you might sell some of your crop to miller as fee for grinding you wheat.. and the wheat you sold the miller was mix with all the other wheat collected... so run of the mill is common, and not pure or perfect... (your wheat would be run through the mill all at one go.. )-- we don't often think about it, but there are many varieties of wheat.. some are soft (cake flours) and some are hard (bread flour) run of the mill would be close to "all purpose " flour.

and mills came in all kinds.. (mechanically; water, tidal, wind) and all sorts of things got milled.. a saw mill (power tools for cutting woods) a flour mill (the kind we most often think of) a steel mil-(would operate bellows, and power hammers; to turn charcoal (pure carbon) and iron into steel-- an alloy) Paper was milled too.. with the mill powering big mallets, to beat the fibers into a slurry for paper), water mills, (either to pump swamps/low lands driy, or to pump water from a deep well) tobacco mills (for grinding tobacco into snuff!) and finally, "mills" as in New England Mills-- power looms for weaving many of these products are still produced in mills... but most mills now are electrically powered.

i think mills refers to a building that houses machinery for transforming power.. (water power become mechanical power.. and in later days, electrical power becomes mechanical..)

rolling mills make things flat (oats come to mind) but mills are great peices of technology-- and could do many things...