MySQL isn't installed on OS X server by default. It is simple to install & setup but you are responsible for applying it's updates. Considering how many sites get attacked via MySQL exploits are you sure you want the responsibility for keeping it secure in addition to the website code? You don't have to be a technical genius to run a server, but if you are responsible for it you need to dedicate time to maintaining it & updating the packages installed. You can use the built in PostgreSQL DB instead to stay with the Apple installed software.
3. You are asking for simple update management from Apple plus the ability to update to newer versions of some third party packages without things breaking via Apple updates. They are mutually exclusive.
Apple release updates to their software & for the bundled libraries/ packages from third parties. Apple's own PHP may be enough for you, it really depends on what software platform you are actually going to host.
If you stick to using Apple's web software built into server (basically a Wiki) you will be fine. If you need to run any other third party software such as Wordpress, Drupal, Joomla etc then you will start to need to add extra software libraries and make changes for certain features that may get overwritten by system updates. Server is better at managing this than OS X Client but even so the solution is to backup before applying updates & to know how to restore them when a problem occurs.
4. You are unlikely to ever know OS X well enough to manage a list of 'files to change' because the OS X server UI will edit the config files behind your back. Look at a clean installed OS X disk, hundreds of thousands of files. The best you can do is read the manuals & read the sites that discuss server setup (or get a job as a system admin & spend years learning).
Sorry, I'm failing to see how you can want to make a website that runs on 'a wide variety of hosts' and then pick one of the most niche platforms to use as a web server. OS X has it's own way to build & install software, fewer users do this on a server compared to other OS's used for web hosting, it means less help on the web. It also means issues take longer to resolve. OS X doesn't even register most of the time if you look at statistics for web server OS usage.
It looks like you are trying to look at a 'big picture' where you manage everything. Starting with the server is not a simple way to make a website. What's the point of all the extra work? Build your site & use any of the millions of existing web hosts, learn how to manage a website then you can move from any host to another. The server choice should be ancillary.
Third party hosts will keep your software up to date, manage the firewall & do many things that you need to manage if you self host on OS X. Have you considered all that?
