Thanks, that’s interesting. I thought I was generating a new taxonomy with the function above. I looked around and I ended up finding https://wordpress.org/plugins/acf-advanced-taxonomy-selector/ which allows me to use specific categories for the CPT and not have them appear anywhere else, and which works with the function above. So that’s what I was looking for.
And wsing'meta_box_cb' => false does remove the category metabox while leaving the menu item in admin, and works with the plugin and function above.