I didn’t mean audio filters but you’re probably using Kega, right? Might want to check Genesis Plus GX core in Retroarch. See the docs here: docs.libretro.com/library/genesis_plus_gx/

By an off chance it’s also possible that something weird is happening to sampling rate, like your digital output only works at 48khz while Genesis outputs 44khz. Makes it sound horrible for sure. Happened to me on some occasions on Mac with a modern USB-C display recently (but like in general and not emulators).

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Mega Drive/Genesis FM[genesis_plus_gx_ym2612]

Select method used to emulate the FM synthesizer (main sound generator) of the Mega Drive/Genesis. ‘MAME’ options are fast, and run full speed on most systems. ‘Nuked’ options are cycle accurate, very high quality, and have substantial CPU requirements. The ‘YM2612’ chip is used by the original Model 1 Mega Drive/Genesis. The ‘YM3438’ is used in later Mega Drive/Genesis revisions.

• MAME (YM2612) [mame (ym2612)] - Selects MAME (YM2612) [original Model 1 Mega Drive/Genesis] as FM synthesizer method which is fast and fullspeed.
• MAME (ASIC YM3438) [mame (asic ym3438)] - Selects MAME (ASIC YM3438) [later Mega Drive/Genesis revisions] as FM synthesizer method which is fast and fullspeed.
• MAME (Enhanced YM3438) [mame (enhanced ym3438)] - Selects MAME (Enhanced YM3438) [later Mega Drive/Genesis revisions] as FM synthesizer method which is fast and fullspeed.
• Nuked (YM2612) [nuked (ym2612)] - Selects Nuked (YM2612) [original Model 1 Mega Drive/Genesis] as FM synthesizer method which is high quality but has high CPU requirements.
• Nuked (YM3438) [nuked (ym3438)] - Selects Nuked (YM3438) [later Mega Drive/Genesis revisions] FM synthesizer method which is fast but has high CPU requirements.