I was going to say the patch cable setup was just a passive aid to take the Mega Drive I's minijack stereo output (the big DIN AV connector on the rear only does mono) to a more serious two RCA jack setup. But looking at a schematic to check, it does do more stuff, and apparently connecting the patch cable will reroute stuff so the sound mixing is done on the Mega CD side, not the Mega Drive side (early Mega Drive revisions are somewhat infamous for showing that Sega hadn’t quite mastered the dark arts of analogue sound circuitry).
(I would double check some of this, but my Mega Drive / Mega CD setup isn't to hand, and the CD drive is broken anyway, although I understand the JP/PAL piano tune on the logo screen is all from the Mega CD side?).