Can PhpStorm be configured to recognize functions as used when called via callbacks or as methods of an object?

A method of the GCS_Sermons object appears as unused:
public function most_recent_with_taxonomy($taxonomy_id)
But is used by the most_recent_sermon() method in the object GCS_Taxonomies_Base:
return $this->sermons->most_recent_with_taxonomy( $this->id );

Do I get right that Ctrl/Cmd+clicking the method call doesn't bring you to the method definition? Not sure, maybe class definitions are resolved wrongly, hard to say without looking at the project.

Sometimes a function only used as a callback appears as unused. For example:
public function plugin_options_validate( $input )
Will appear unused even though it is utilized:
register_setting( $this->plugin_option_key, $this->plugin_option_key, array( $this, 'plugin_options_validate' ));

This is hard to support. We've tried that with namespace and class names, that was the result: https://youtrack.jetbrains.com/issue/WI-43858

Anyways, please vote: https://youtrack.jetbrains.com/issue/WI-27761

Strangely enough on other occasions the function will be correctly denoted as used, for example the following function and callback:
function lqd_customize_register ( $wp_customize )
Which is only used here:
add_action( 'customize_register', 'lqd_customize_register' );

This is something the Wordpress plugin takes credit for, it's easier to make references for add_action() than for every possible way of calling a method.

https://github.com/LiquidChurch/lqd-messages/blob/major-04-22-20/includes/post-types/class-sermons.php (see line 594 and following)

PhpStorm doesn't know what the $sermons property is, you might wanna type-hint it with the PHPDoc @var tag.