The retail game comes on a GD-ROM, which has a higher capacity than a CD-R. The game won't fit on a CD-R without shrinking the content somehow.
If you already own the GD-ROM, then why do you want to make a CDI? Either use the GD-ROM, or rip it to GDI format if you want to play it on GDEMU.
"Fear the HUnewearl."