Rim 'dish' won't matter. If the wheel is in the frame square and it's true that's all that matters. It could be off center to the left or right, but as long as it's true and the axle is in the dropout properly it won't matter. The rim is supposed to be something to use to judge whether something else is parallel to it. The rim being centered doesn't matter at all...if it did using various wheels w/ different rim widthsto align a hanger wouldn't work. The ONLY thing(s) that matter are the plane of the rim. Doesn't matter where it is. That's why hanger alignment tools have an adjustable 'feeler'.
For the OP's question...I don't think a hub could be 'misaligned' and make into a completed wheel and on a bike. Well, I guess anything is possible but this is a helluva stretch.