No real discernible differences in audio quality(to my ears)...but as you say,the instrumentation is noticeably different.
In 1990 I was in the fortunate position of being offered an ex shop demo DAT recorder at less than half price. This meant I was able to make recordings of much higher quality than most people around me. Also, because the DAT format is 18 bit rather than a CDs 16 bit I decided to record 6dB below peak level, still giving me a better noise floor than the hardware synths but also plenty of headroom.
By 2000 or thereabouts this machine was starting to get unreliable so I transferred all my recordings to the computer and stored them as flac format. A couple of years after that ZynAddSubFX first appeared and the rest (as they say) is history
