holy thread resurrections, this thing is ancient.
Anyhow, as far as I know, the correct answer is there isn't any difference between the AGA fixed version on disk that Magnetic Bytes shipped and the one on the CD32 Lotus Trilogy. I seem to remember playing the CD32 version on my A1200 without doing anything unusual for the time. (Maybe booting the 1200 with no startup script and assigning libs to a directory containing the A1200 version of lowlevel.library and nonvolatile.library or something before running the CD's startup-sequence, but that was it. A really old trick that boots most CD32 games on an A1200.)