Not many replies John, likely due to lack of alignment specialists. I can only offer a few thoughts. Are the hangers possibly bent/damaged, since the original axle was bent? Axles are normally bent upwards, with the peak in the center. If this peak differs front axle to rear axle, that would bother me. I would be happier if the new axle was 1/4 inch short on each end, making the axle bend, more centered. In this case, I'd say it won't matter long term.
I can't answer your question "will it matter", but if mine, I would search out an actual tech for correct info, to satisfy my perfectionist obsession. :)
Jerry