I would recommend, for dumping code.bin, to use GodMode9.
Use whichever one of the last two tutorials that you need:
https://gbatemp.net/threads/title-dumping-and-file-extraction-using-godmode9-1-0.465427/ (Note: The titled used is the same one as before)
Instead of copying over the data in the romfs, just copy the .code in the exefs folder.
Now, install devkitpro and git, then place the code.bin in the smash folder in a clone/downloaded version of this repository:
https://github.com/shinyquagsire23/SaltySD
Once you have that done, open MSYS, navigate to the smash folder in the SaltySD folder and type in "make".