I added a limiter to the output and an envelope to my synth object, but after a bunch of experimenting with different settings for each, the flatlining effect was still there. Throttling beyond the note+release's duration did fix it, but that also removed the layering effect of overlapping chords. I think some of those were interesting and wanted to keep them. The last thing I tried was setting the attack to 0.01 and I think that fixed the flatlining issue?
It seemed like the source is minified, but I didn't look that closely -- I'd be curious to hear more about your sonification scheme.
Edit: nevermind I found a link to the source & explanation in another comment! https://github.com/tevans-3/synesthesia
I know this doesn't help you now, but I changed the default volume to be significantly lower...
I adjusted the default volume, so that "painfully loud" is now opt-in by default...