ACF uses the built in wp_list_categories() function to show terms as checkboxes. I don’t know if you can alter the arguments for this function to do what you want. Here is the code from ACF
// vars
$args = array(
'taxonomy' => $field['taxonomy'],
'show_option_none' => sprintf( _x('No %s', 'No terms', 'acf'), strtolower($taxonomy_obj->labels->name) ),
'hide_empty' => false,
'style' => 'none',
'walker' => new ACF_Taxonomy_Field_Walker( $field ),
);
// filter for 3rd party customization
$args = apply_filters('acf/fields/taxonomy/wp_list_categories', $args, $field);
$args = apply_filters('acf/fields/taxonomy/wp_list_categories/name=' . $field['_name'], $args, $field);
$args = apply_filters('acf/fields/taxonomy/wp_list_categories/key=' . $field['key'], $args, $field);
?>
<div class="categorychecklist-holder">
<ul class="acf-checkbox-list acf-bl">
<?php wp_list_categories( $args ); ?>
</ul>
</div>
