Bypass “supress_filters” in WP Query

Looking at the WP_Query Class you should be able to use pre_get_posts to modify the query before any other filters are run, which includes turning off the suppress_filters flag. An example of this could be:

/**
 * Modify WP_Queries
 * @link https://wordpress.stackexchange.com/q/356950/7355
 *
 * @param WP_Query $query
 *
 * @return void
 */
function wpse356950_query_modifications( $query ) {

    // Don't run on admin
    if( is_admin() ) {
        return;
    }

    // Some conditional to tell our query from other queries
    if( $query->get( 'suppress_filters' ) ) {
        $query->set( 'suppress_filters', false );
    }

}
add_action( 'pre_get_posts', 'wpse356950_query_modifications' );