You are not flashing your DS with a Passme option, what you are doing is bypassing the DS's firmware protection temprarily and booting the Slot 2 device instead of the Slot 1 device. Passme is how the older flashcarts (e.g., Superkey and Supercard) used to work. The Superkey was the Passme device which bypassed the DS's firmware checks booted the Supercard located in Slot 2 which was the real flashcart containing the OS. This method was necessary back then, because the copyright protection on the DS was not fully cracked, and the only way to boot the OS of the flashcart was as a Slot 2 device. The flashing of the DS firmware (which was done using a method called Flashme which involved opening with your DS battery compartment to short out a contact to run the flashing code) was already pretty much unnecessary by the time the Passme devices emerged (except for the ultra paranoid worried about their DS being bricked by a homebrew trojan, and needing a way to recover). What the flashing did was basically embed the bypassing code permanently in the firmware of your DS so that the Slot 2 device will boot.
With the newer flashcarts, both the functions of the Passme device and the Slot 2 flashcart are combined into one unit. If you do have an older Slot 2 flashcart laying around, Passme option will allow you to boot it temporarily. Neither modify the DS's installed firmware in any way.