I've been thinking about this too, with regards to whether it's kosher to allow it to be linked here on NeoGAF, and I don't have an answer because I don't know what is actually distributed in the patch files.
Pretty sure yellow.pkg is all of the games files, Sky says so himself in the OP of his gba temp thread. His merging files has a new one to replace one from one of the umd. Don't have my copy yet but I think it's pretty obvious how it works. If I'm right the new pkg file contains the data from both umds. The rest of the files you replace seems to be a bunch of icons and the file hierarchy descriptor.
I doubt you are downloading 1,5GB of dummy files.