I believe it’s because the field uses wp_get_object_terms() to get the taxonomies for the field and uses get_terms() to get the taxonomy list. You can take a look at the plugin core file here “wp-content/plugins/advanced-custom-fields-pro/fields/taxonomy.php”.
I’m not sure how CPT-onomies works, but maybe you can’t get the taxonomy using wp_get_object_terms()? Please ask the plugin author about this issue.
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