I'm not entirely sure how saving in Goomba Color works, it might have the same problem as in Lameboy. The basic idea behind the glitch, IIRC (haven't played Pokémon since Silver) is to turn off the Game Boy during a save after performing some Pokémon movement between storage boxes on the (in-game) PC. This way the Pokémon you moved stays in its original box, but is also sent to receiving box, thus duplicating it. It works because the Pokémon is first copied to the new box, then deleted from the old box. By turning off the Game Boy after the copy but before the delete, you clone the Pokémon.
The problem is that you can't turn off your DS mid-save in Lameboy, since the save only exists in RAM, and turning it off means you lose any changes. Turning it off while Lameboy copies the save to your microSD won't do anything either, except possibly corrupt your microSD, since at that point, the changes have already been written to the save in RAM; your aim is to stop (some of) the changes from being written, and stopping Lameboy from copying your save won't help that at all. If Goomba Color's save process is anywhere near analogous to this (and I believe it is), it won't work in Goomba Color either.
EDIT: Clarify for non-Pokémon players.