I've had both the TB's off of our 2.5 TJ's, no real noticable difference in size that I noticed but then I did not have a 4.0 sitting next to it so there might be a difference but I don't think so, all the sensors are the same. Perhaps you are thinking about a bored out throttle body from the aftermarket ? There is not a whole lot you can do for power in the 2.5 without adding ALOT of hardware up to and inlcuding a super charger.
You could check the part numbers online for a 4.0 TB vs a 2.5 and see if they are different.
Just to warn you, we have some posting nazi's here that get really irate if you post other than mj/xj questions on this one. Use the other tech, you will find TJ and YJ stuff posted over there. I just happen to be a member who has both XJ's and TJ's...