I did a audio comparison of a SN76489 (left) and SAA1099 (right) recording using a tndy nano v1.0 card by matze79 that's built around an SN76489 and a soundblaster 1.5 with saa1099 addon. I used sbvgm.exe v1.33 by to play a list of music since it support both cards. I added a pause in between each track so I could re-sync the audio in between each track. Since I did not want to add mp3 compression artefact I saved a 44.1khz 16bit wave file. I wanted to make a new playlist but I could not find enough new music for it, so I re-used the one I made already with the addition of WonderBoy3. Maybe it will help us understand the audio problem with the bass note on some music. I think it is apparent in the phantasy star and y's music again, but I think you are aware of that problem and just need some time to address. Other than that I think the tone and timing resemblance is very convincing but there seem to be some amplitude difference in between some instruments so it's hard to balance stereo signal. Since the file is around 90mb I will put it on 💾 google drive.
Here is the lineup:
Alex Kidd in Miracle World - 04 - Underwater.vgm
Choplifter - 02 - Round 1.vgm
Gunstar Heroes (GG) - 04 - Choose a Path.vgm
Gunstar Heroes (GG) - 08 - Rolling Chaser.vgm
Lord of the Sword - 04 - Story.vgm
Miracle Warriors - 04 - Castle.vgm
Phantasy Star - 15 - Medusa.vgm
SpellCaster - 05 - Forest.vgm
Wonder Boy - 04 - Boss Round.vgm
Ys - 05 - First Step Towards Wars.vgm
Wonder Boy III - 10 - The Danger Zone.vgm
While I had everything open I'll make a spectrograph of Ys since the bass problem seem to be more apparent here. Maybe it will eventually be of any help. It's a zoom of the first 2 seconds 0-4khz frequency of Ys with the SN76489 on top, SAA1099 in the middle and the difference in bottom. It look like where there is supposed to have a mute the bass line get to be played too loud... or something like it. I'm eager to have your opinion on that.