I would think that they would absorb the stain at a different rate, resulting in darker or lighter coloring between the three. Is finishing in clear an option?
I would really like to do the top in a dark stain. Would the table not look right if I did the aprons and the legs in just a clear? And by clear do you mean like a Danish oil or something like that ?
The aprons & legs are on a vertical plane. Top is on a horizontal plane. Light play off these planes differently. The apron for example will be in the shadows of the overhanging top. Make a quick mock up with some scraps & stain both pieces at the same time. Hold them in the room at the correct level & look them over.
Always test your finish on scraps 1st. It's the "Measure twice cut once." rule for finishing IMHO.