In snes files, 00000001.app is the emulator.
The file .pcm in the 00000005.app is a pack of samples. In Virtual Console, most (if not all) snes games don't use original samples from the rom, but new samples in the file .pcm. That's why the .rom file is not exactly like the rom you can download from internet, because it's modified to point to this samples. I injected the original DCK rom and really notice no difference on sound, but who knows.
Anyway, you can inject a rom of ANY size on ANY snes VC, so you can play all games at 60hz on pal consoles if you inject a rom to gradius or picross.
I tried it manually with DCK in gradius and worked very well.
I'm currently building a tool for doing this, but still on development.
Ah, and I tried Yoshi's Island and it didn't work, so probably FX it's not supported... at least FX2.