Hi. Pointing both of the symlinks you mention to the zimbra postfix/sendmail binary seems to have solved the problem. I'm getting my notifications now.
I've stopped/restarted zimbra and my independent installation of MySQL several times and they are working well. Amavisd is running. I can send and receive mail to zimbra. All seems well, but because of your warning I will keep an eye on it for problems. Admittedly, it is not under heavy load yet. I haven't started sending any heavy mail yet.
One thing that I might be doing different than others is that I manage my server through Webmin; that includes MySQL. The webmin config for MySQL allows you to put in explicit paths for various settings and resources, and since i have two MySQL installs on this server I have been explicit in Webmin as to which MySQL it should be controlling. Perhaps, along with that, certain parameters are being passed to mysqld when it starts that tells it where everything is. I was thinking about this last night, considering that mine was working with the entry at the bottom of ldloader when the original poster suggested that this shouldn't work. Maybe it's the Webmin setup, and starting MySQL through Webmin, that's making it work correctly? Just an idea.