There is absolutely no problem in using MySQL for other purposes.
Zarafa the web email client is superb and installs all the php stuff you will need.
I have a habit of installing webmin as well as it gives just a few things extra in terms of DB and online file manager.
You have to give a disclaimer with webmin be carefull as your changes could conflict with zentyal.
This is really for noobs to say don't do something stupid and then rant your server is broken.
The zarafa install gives a good example of security rights.
The mysql password is stored in the zentyal config files. Each application database should have its own user as running all as root is frowned upon due to security implications.
The only thing I don't like and this is nothing to do with zentyal. Zentyal provides everything in one box which is brilliant.
From a sysadmin who runs in the middle of SMB this means the services don't have the isolation of preference as things can come down like dominoes.
As I say for me there are two bits missing from my own Zentyal perfect world.
Webmin and
http://lxc-webpanel.github.io/index.htmlBoth are a doddle to install.
lxc gives me the isolation to install other applications.
lxc is somewhere between a chroot and full hypervisor.
Basically virtualisation with a tiny memory and resource footprint isolated at a network level.
https://www.docker.io/If you want a super simple higher level abstraction of LXC.
Anyone with zentyal I suggest take a look at the above.
Also the last bit in the jigsaw and its an obvious but the free M$ RSAT Remotes Server Administration Tools for those of us stuck with win clients.
Zentyal isn't a replacement for SBS, its much much more.
PS I do dabble with Microsoft and I was a fan of SBS if you are thinking of 2012 Fundmentals I had to think what does it exactly do apart from create a domain. The license is a catch aswell, I presumed concurrent users but its 25 configured users. At the end of 6 months I realised what it did was annoy. So ditched and there are two choices ClearOS and Zentyal with Zentyal being my preference.
/var/lib/zentyal/conf for mysql password and others
you might need to install apt get install bridge-utils libvirt-bin debootstrap for lxc also do a reboot for the networking
lxc-console -n myfirstcontainer to ssh (the defualt ubuntu template user=ubuntu password=ubuntu)
ctrl+a q to quit
If you look at the image you can see how slim LXC is by sharing the kernel.
This way you can install apps, kill the distro without affecting zentyal.