Approach on how to create a multipage website with PHP - MYSQL custom admin panel

It really depends on what you’re trying to achieve. Maybe easiest way is to install WordPress and use a combination of theme and plugins which fits your needs.

Not sure what you actually mean by that. Any website runs on a webserver.

You can set folders to be read-only, no security risks at all.

It really depends on your goals
I would suggest picking up a PHP Framework (I personally recommend Laravel) and create what you need. It will be the best choice.
Try explaining more detailed what you’re trying to achieve and maybe better to ask on dev forums, such as stackoverflow.