No it wont make any difference once the car was available with the running gear from the factory, NA-Turbo SR20, NA-RB25 R34, NA-1JZ Turbo Chaser etc.

Big difference if your throwing an engine not available as a factory option IE: 2JZ into a chaser or 1JZ into a silvia or as graham found out a RB26 into a gts-t/gtt skyline vrt wise.