No. ACF will not use the append flag. The problem with the append flag is that if a term is removed from a taxonomy field and save/load terms is turned on that no terms will ever be removed from the relationships created by WP. This question has come up in the past. The only solution is to not use save/load terms and create your own acf/save_post filter that does a check of all the taxonomy fields involved and then add remove terms in WP yourself.