Where to place hook script for plugin

New to WP, but a fairly experienced PHP coder.

I’m using a plugin which offers a few hooks which allow me to place additional content in the head/content/footer (this is a plugin which generates it’s own complete page structure).

It’s clear to me how the ‘add_action’ hook is used, but what I’m trying to understand is where the best place to add these hook scripts such that they would not be overwritten by a site or plugin update.

I thought about putting it in the theme/functions.php, but then soon realized that this script may not be invoked when this plugin is active (it is a ‘maintenance mode’ plugin). I also want these hooks to persist regardless of what theme is in use.

Does WP core offer any kind of ‘custom-functions.php’ script which if present, is included during site initialization, and would not be overwritten by an update?

Thanks!