apply_filters and do_action are NOT stored in $wp_filter, ONLY add_filter and add_action are stored in $wp_filter
When you call apply_filters or do_action, core WordPress loops through all of the registered filters or actions (added by add_filter and add_action), looking for any matching ones, and then executes the associated function.
The only difference being actions which are stored in the $wp_actions global var
These are the global vars available for hooks (actions/filters):
global $wp_filter, $wp_actions, $wp_current_filter;
$wp_actions – stores actions that have already been fired with the number of times it was fired, each time do_action is called this number is incremented.
You can look at the Query Monitor plugin which does handle tracking of hooks (actions/filters):
https://github.com/johnbillion/query-monitor
Now with that said, one option you have that you can do, is to add your own action for the all action, and then collect and save the filters/actions that are ran yourself.
Here’s some sites that talk about this:
https://www.smashingmagazine.com/2012/02/inside-wordpress-actions-filters/
Here’s example code of doing this:
https://gist.github.com/bueltge/1000143
https://developer.wordpress.org/plugins/hooks/advanced-topics/#debugging-with-the-all-hook