To the best of my knowledge it is because of how the operating system is setup for the Nook STR. It cannot boot off of the SD card. So what happens, AFAIK, you are loading the new firmware/OS on to the SD card which then loads it in to main storage pool used for holding the OS and firmware when you reboot it. To get back to the original Nook OS, you have to reload it back on to the SD card which goes through the same process of loading it to the main memory OS storage pool overwritting what was there.
So you can't boot selectively off the SD card. You can (so far and AFAIK) only have a single OS/firmware configuration loaded to that SD card, which overwrites what is on the nook STR. Simply removing the SD card doesn't change what is written to the nook STR already. So no way to select between OS configurations on the SD card, and whatever got loaded up the Nook STR is there until you load in an SD card with a new firmware/OS configuration.