When you run MAME (I mean regular MAME on a PC), you tell it what game to load and MAME itself knows what files to look for, how to load and combine them, and what hardware to emulate (that's the answer to your question "Is each game differently treated by MAME?") The ROM files themselves don't have any headers or other information that says what game they're for or how to load or emulate them. They're just raw data dumps. So there isn't anything you can do to the ROM data embedded in the ELF to make the PS2 emulator magically recognize it as Gyruss (or whatever game) and run it, even in the unlikely event that the MAME code to emulate that game is still there.
Well explained, you have well convienced me
Now, for the last question: Is there any interest in the original embedded rom and if yes where to submit it?
After do some reading on the roms and the tools used(just taking a quick look) I see that there can be different revisions of the rom , corrupted rom dumps(due to dust etc on the hardware) or different version. Forgive me if I get the terms wrong.
The dump I download has two dump files. The first is a complete match and the second is equal in size but the contens are different. This makes me believe that either the rom in the emulator is a different revision, different version , or the correct dump. The reason I say the correct dumb is because Konami oficially gave rights to this HAMSTER company to emulate and I highly doubt that they used tools to make dumps but Konami supplied the rom, so it must be a correct dump. Other than that there is also a SOUND folder which I suppose that contains music and effects. The files in there are in .ADP format(not sure if familiar to you). Although it is possible they are in another format and the extension means nothing and the sounds were optimized and played differently from the emulator. I can play them with some tools but I have to tweak around to find the right frequenzy.