this is assuming the only thing the server is running is linux apache mysql and php; but you'd just write your PHP code and create a package like an RPM or what have you, that deploys it to the right place, and your configs for the rest of things would also either be their own packages, or managed by some script or puppet.

It all depends i guess. I suppose it probably is much easier to manage if you just compose some images, than if you say "you gotta configure the machine" because if you can abstract away much of that stuff into containers then you're not stuck on one distro of linux, so i get why people use docker (which I call dorker btw).