Two ideas:
1. Put the G4 drive in an external enclosure to plug into the G5 machine after bootup (no boot conflicts this way).
2. Rename and change the boot priority of the G4 partitions so they won't conflict with the G5. i.e., if the boot/SYS: partition on both machines is DH0, change the G4 device name to SDH0, and make sure it has a lower boot priority than the G5's boot partition. You might have to change the volume names as well, and of course you can change the partitions back to their old names once the copy is complete and the drive is back in the G4.