Time to find out what is really going on here
I took the Outrun 2 CHD from MAME, extracted the two images (512MB/1GB), decrypted them and then extracted the files from each of these FATX images files and compared them.
The contents were exactly the same!
So I started looking at the two images, using your favourite hex editor open up the two files and search for: boot.id
In the 512MB image you will find it at: 0x11000
In the 1GB image you will find it at: 0x21000
Then I took the 1GB image and removed 0x10000 bytes before offset 0x21000.
>md5sum OUTRUN2_1GB_D.BIN OUTRUN2_512MB_D.BIN
5f11ebe526af10b8989fe38a0dbbba59 OUTRUN2_1GB_D.BIN
5f11ebe526af10b8989fe38a0dbbba59 OUTRUN2_512MB_D.BIN
If you remove these 0x10000 bytes the FATX images are
exactly the same!
I did the same test with: Outrun 2 Special Tours and the result is exactly the same.
It looks like if the: boot.id is found at: 0x11000 it's a 512 MB game.
This means that: Outrun 2 Prototype is for a 512 MB setup.