The different channel assignment in the G3 system is to keep similar functions close together to reduce any type of lag in the system. If you use the G3 channel order on a PPM or PCM1024 system, then functions such as dual elevators will have the minimum lag between the halves. The same for separate aileron servos.

Of course, the much faster processing of the G3 system also helps a lot!

If you're going to be using a trainer cord with other systems, though, you'll need to make sure the channel order is the same for both the student and master transmitters. With the Futaba 12FG, 12Z, or 14MZ, you can make the channel order whatever you want, regardless of whether you are using PPM, PCM1024, PCM-G3, or FASST transmission.