The notification email setting is used in the From mail header (RFC822), but (as you note) for this purpose you want to set the Envelope From that’s used in the SMTP transaction (RFC5321). Discourse uses reply_by_email_address here.
The most integrated solution is to set the reply_by_email_address to something that gets delivered back to Discourse so that it automatically handles bounces. That’s what we do on our hosting platform.
I’d suggest reading through this: Configure direct-delivery incoming email for self-hosted sites with Mail-Receiver