The objective is to ensure that when editing a post, the metabox that lists a hierarchical taxonomy doesn’t reorder itself upon Update to put checked items on top.
Right now, edit-form-advanced.php calls add_meta_box(), passing a callback of post_categories_meta_box, which is defined in meta-boxes.php.
post_categories_meta_box() invokes wp_terms_checklist(), leaving the checked_ontop parameter undefined. wp_terms_checklist() defaults that parameter to true, which is the root cause of all this hooplah.
Nary a filter hook to be found anywhere along the chain until we back out and discover add_meta_boxes and add_meta_boxes_{$post_type}.
The only solution I was able to come up with myself was to hook onto one of these actions, globalize $wp_meta_boxes, and replace occurrences of the post_categories_meta_box callback with a callback of my own, where I completely duplicate all of post_categories_meta_box() and simply add the parameter 'checked_ontop' => false.
Works. But fugly. This seems ridiculous – is there no more elegant way to simply let your hierarchical taxonomies keep their order in metaboxes?
There’s a plugin written specifically to fix this ‘feature’ of WordPress, it’s called Category Checklist Tree. Despite the name, it works on custom taxonomies too.
Nowadays there is a hook available for this problem:
https://developer.wordpress.org/reference/hooks/wp_terms_checklist_args/