When you install some mods you drag certain files into your game directory and replace the files.

Other mods, though, come with an installer where you can set parameters first.

Does the installer then go and automatically replace the certain files? At the end of the day, is that all the installation of any mod is?

Is the installation of a mod simply the replacement of certain files inside the game's root directory?

Do mods exist which don't fit the above statement? That install outside the game's root? Why do they do this?

All the mods I can think of do just replace certain files inside the game's root. However, I know Team Fortress was spawned from a multiplayer halflife 1 mod. Do you reckon that mod installed files outside the root to enable multiplayer via a network for a single player game?

How rare are these mods? Or do they not even exist? Do even extensive mods make all their changes inside the root?