Yeah, I should re-write that part to make it clearer.
You initially need the flashcart or the neo-key in order to flash the menu onto your mk2/mk3 directly. The menu is a program that runs all your applications/roms.
Once the next flashme comes out (I don't know when), you should be able to remove the flashcart/neo-key from the gba slot. This is possible since the next flashme should have code to boot the mk2/mk3 directly (since the menu is now stored there).
So, you DO need the flashcart initially to install/run the menu, but once the next flashme comes out, you will no longer need the flashcart in the gba slot (except in unusual cases where the menu on the mk2/mk3 becomes corrupted, then the flashcart will be used momentarily to recover a previous working version)
BruceG