The overall bitterness should be the same. The amount of isomerized AA's should be about the same if the calculated IBU"s are the same. The flavor and aroma profiles, as you noted, will be a bit different.
However, since the times different varieties and amounts of hops are boiled changes, you may get a slightly different bittering characteristic. Different varieties can add slightly different bittering characters to the beer - generally varying on a 'harsh' to 'soft' continuum. I doubt the changes here would make a very perceptible difference, though.