In Jira you can have notifications come from different from addresses depending on what project they're in. So, you do set up a default from address when configuring your SMTP server under Administration --> Mail Servers, but it can be over-ridden when administering a specific project.

I found that if I used an SMTP server configured completely in via Jira's web interface (not using SSL), this worked as I would have expected. Notifications came from the address specified on a per project basis.

On the same data set, when I deleted that mail server, and switched it to a gmail SMTP configuration (JNDI), the email address I specified in the JNDI configuration always overrode the project specific settings.