The Black Mill quest mod is a great mod that adds some mills, but I guess not in the way you mean, because they act more like "dungeons" and / or are integrated in the quest line. So they fulfill a function and are not just eyecandy.
Quests with them would be fine, honestly, may main concern would be to get more of them in the game than just the random couple of them (stickler for consistency and such). The look of them (sans any retexturing) seems rather Imperial in nature, so seeing them logically placed about some of the Imperial settlements might make for a nice touch.
Since I am unfamiliar with the Black Mill mod, how many does it add and in what kind of placement method?