Can PHP cron work with standard WordPress hooks?

I was trying to schedule a cron job from within functions.php, but it wasn’t working so I pulled the function into a PHP cron job, and then added a line to run the function right after that.

I saved this as an event in WP Crontrol, but the function I wrote includes wp_update_post and wp_set_object_terms My question is whether PHP cron will work this way, when the PHP code is separate from my functions. Can it use WordPress hooks?