You are what you are, so yes, height is certainly part of the equation as it is fundamental to someone's body...why should any physical characterisitics be normalized for? Jordan was quite tall as well so, comparatively, he would not be at a severe disadvantage relative to Wilt.
Jordan's height and longer arms and larger hands didn't necessarily help him excel in baseball, maybe defensively in the field. Couldn't those characteristics have given him an advantage at hitting a baseball, greater reach with the bat to get to the outside curveball he couldn't effectively handle (to at least slap it to right field or just foul off to reduce the number of Ks)? Maybe, maybe not...there were other factors associated with hitting that he couldn't master well enough.
But I wouldn't even use his time playing baseball against him in judging his athletic prowess because he could have just as easily never bothered to give it a shot and we wouldn't know whether he would have been great at it. Just like we don't know how great of a football player he could have been if he tried to make a go of professional football instead of baseball. But his baseball exploits certainly demonstrate his competitive spirit, for which he had very few or no equals.