As long as you release the Shift-Command-Option-E-[partition #] key combo after the Mac did detect the boot partition (Happy Mac appears) you should not have any side effects from the HDT trick (no forced desktop rebuild).
editional information: To trigger a desktop rebuild just hold the option key depressed upon mounting a volume. This works for any write enabled volume (like harddisk drives, Floppies, ZIP media etc.), no matter if mounted at boot time or later.