The wristpin is moved up according to the rod length and difference in stroke, but as far as the overall height I believe they're typically the same.
Taking a 383 piston, 5.7" rod for example... you use half of whatever the stroke is because half of it moves the piston up in the bore, and the other half moves it down (not sure if you got that part, some understand it & some don't). The difference in the two is 0.27" (3.75"-3.48"), and since we're working with a 5.7" rod you only use half of the 0.27" (0.135"). If you were running a 6" rod you would move the wristpin up another 0.3", the reason is the piston will be 0.3" higher in the bore, whether it's at TDC or BDC...
Part of the reasoning behind a 6" though comes in everywhere between TDC and BDC. The piston moves faster up & down the bore, there is also less cylinder wall loading... these are just a few details, the topic is kind of like turbo vs. supercharger, everybody has an opinion and will build their engine different. There isn't quite so much of an advantage comparing a 5.7" to 6.0" rod, but when you look at a stock 400 rod (5.565") vs. 6.0, that rod/stroke ratio looks a whole lot more enticing.