Yes. You can create as many bootable partitions as you like. The one that actualy boots is choosen from the boot priority: the partition with the highest priority in the system is used. You can overide this choice in the early startup menu.
But the choice is not permanent. You have to choose again every reset. Note that OS3.9 resets two times, so you have to choose the OS3.9 partition twice.
And a reset does not remove the OS3.9 rom update from memory, so if you choose to boot from the 3.1 partition you might still run with scsi.device V44, exec V44 etc., everything that is reset-proof.
Bye,
Thomas