The 3 port pipe usually has 5.0mm stinger outlet and the 5 port pipe usually has 5.2mm to take advantage of the Rules.
Both pipes can be used on either engine, but the 5.0mm stinger had better be on your 3 port engine if you are racing by the roar rules and are being teched!
Ex pipes are designed with the Ex port Dia. and port timing duration in mind, not the number of transfer ports. The only differences in these pipes should be the stinger.
BK