So I found a solution that made it work for me. I noticed that all metaboxes are added in ‘high’ priority, except those positioned on the side. Luckily there is filter in ACF to change this. So I changed the priority to ‘core’ and the remove_meta_box started working.
add_filter('acf/input/meta_box_priority', 'custom_meta_box_priority', 10, 2);
function custom_meta_box_priority($priority, $field_group) {
$priority = 'core';
return $priority;
}