Modify custom post type after it has been registered was closed a year ago but didn't answer how to modify labels and the menu_icon for CPTs. Modifying plugin code is only a temporary fix until the plugins are updated. Most CPT creating plugins I've seen so far do not contain a settings option to customise the labels or menu icon.
As such, I'd like to be able to over-ride or modify the labels array and many of the other arguments for CPTs (created by any plugins) in my theme functions.php file preferably (where-else?).