To hide the standard WP meta box add this setting to the taxonomy, https://codex.wordpress.org/Function_Reference/register_taxonomy
'meta_box_cb' => false,
When setting up a taxonomy field there is a setting to choose a taxonomy you are using.
If you are using the built in Category taxonomy then there isn’t any way to limit the terms to just those used on your CPT. And there isn’t any way to prevent people from selecting these categories for post. If you need terms that can only be used for your CPT then you need to create a new taxonomy for this. That’s just the way WP works.
