Having the same issue too.
We have set up various custom taxonomies for which we are planning to use the ACF interface to interact with, and not the native metaboxes that appear in the sidebar of the edit screen which will become redundant for our purposes.
Yes, we can hide these using the screen options panel but this is not ideal because clients can find this and switch them on, therefore causing potential headaches all round!
It would be such a great feature to be able to remove these from the ‘options’ panel when creating a field group in ACF.
I guess it’s a simple case of ACF being able to read the custom taxonomies we’ve set up for our custom post type, or depending on whatever location rule has been set, and then showing them with checkboxes in the ‘Hide On Screen’ option panel?
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