Do you remember what the exact error message was? I’m not a forum admin here, but I can find one to look at this issue and increase the thresholds then for a better user experience.
What exactly is not working with the notifications? They should work just fine. What notifications do you mean? Push Notifications?
Could you please be a bit more specific on that? What does “wipes out” mean in technical details? What error messages are you seeing? What’s the exact behaviour? The Mattermost application server is very likely not affected by whatever iredmail does, it most likely just stops the nginx proxy or starts a different application on port 443 or the like, so it would be interesting to see what exactly is the problem here then. Does iredmail also use an nginx webserver?
Mattermost’s nginx configuration uses name based virtual hosting as you can see in the config file, so if you access the server using the server_name specified in the configuration file, you will end up on the Mattermost instance and this should not interfere with other nginx vhosts (if there are any).