The sound when receiving new mail is very loud. I have “System Sounds” in GNOME set very low. Is there a setting in Mailspring that I’m failing to notice?
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Unfortunately, no, I don’t believe so. 
There is a (non-trivial) workaround for overriding the sound here: Custom notification sound - #2 by githrdw
I’d recommend creating a feature request for this, or else voting for the preceding feature request.