While i don't know much about PHP and Apache, i do know enough about DB servers and i worked with MySQL and FireBird
If you have any possibility of doing this i would suggest replacing MySQL with PostGres or FireBird because with the latest two you can use Stored Procs and Triggers (and other stuff), but most web companies only allow MySQL
You can connect with any DB server (even MySQL) anywhere in the world, all you have to know is a valid user and a host name wich can be:
- localhost or 127.0.0.1 (for the same machine)
- the server name on a local network(myservpc)
- a web server(www.mywebsite.com or something)
- an IP address
When you access a DB Server with an alias(name) the IP is extracted and used so if MySQL has access to your ports it should work using your website name.
I think it's easier to access you DB than your files but as i said i have more experience with DB Servers

MSX there is no problem in "directly accessing the database" that doesn't happen with most DB Servers anyway, (only FireBird embeded mode) that kind of access is used for local files only.
You can create users and give them what rights you want so they won't mess up your DB , anyway they don't know what the game is doing so it's unlikely they even know how is your DB stored or how to break it :lol: