The "Startup Disk" pane pretty much shows the same behaviour as holding down the option key at boot: it only shows the last backed up partition (Intel or PPC).
Now that I think of it, I can try making two bootable partitions of the same Intel mac using GUID to see if they both show up. If yes, I can repeat the experiment with my PPC mac and APT. If successful, I'll yell at Apple for 5 seconds, get two hard drives for two macs and get done with this
Or is there a better way to go?