I'll have to compare next time I go into the 2 different types.
You might notice the ground-car guys (or guys and gals, at a PC airport) rushing out to move the PAPI forward and backwards for the next approach ... it's impressive how quickly they can change things when aircraft are line-up on the ILS. Of course, in low-vis conditions, you probably won't see the car.
Seriously though - seeing as the PAPI at ML (as an example) is the standard 3 degrees, the difference must be due to the PAPI being located a little further down the runway - seeing as it is a longer runway, the touchdown zone (with markings and PAPI) is further from the threshold.