v1.15.0 does include the ability to provide custom headers during the setup process but it does not appear to save them. I fill them in, enter my server and password and hit connect and the connection fails. Opening Custom Headers again and they're gone. I can enter them as many times as I want and they never seem to be leveraged during connection.
bluebubbles-latest.log shows when the GET request goes out and Cloud Flare returns "Access Denied" which implies the custom headers are not being sent.