Seperate site search from GD v2 search

Try this:

/**
 * Exclude GD CPTs from WP Search.
 */
function gd_snippet_wp_search_exclude_cpts( $wp_query ) {
	if ( is_admin() || empty( $wp_query ) ) {
		return;
	}

	if ( ! ( $wp_query->is_main_query() && $wp_query->is_search() ) ) {
		return;
	}

	if ( geodir_is_page( 'search' ) ) {
		return;
	}

	$in_search_post_types = get_post_types( array( 'exclude_from_search' => false ) );
	$post_types = geodir_get_posttypes();

	if ( ! empty( $in_search_post_types ) && ! empty( $post_types ) ) {
		$search_post_types = array();

		foreach ( $in_search_post_types as $post_type ) {
			if ( ! in_array( $post_type, $post_types ) ) {
				$search_post_types[] = $post_type;
			}
		}

		$wp_query->set( 'post_type', $search_post_types );
	}
}
add_action( 'pre_get_posts', 'gd_snippet_wp_search_exclude_cpts', 10 );

You can add that as a snippet with the code snippets plugin:
https://wpgeodirectory.com/docs/useful-plugins/#snippets