There are a lot of plugins that add fields to that list. Many plugins use field names that start with an underscore which hides them from that list. I think this was suggested for ACF, but it would seriously effect backwards compatibility and would likely be a nightmare to include a way to update from the current names to new names if it were to change. I’m not the developer so I can’t say what’s involved.
If the custom field meta box is not something you want the client to see you can remove it. https://codex.wordpress.org/Function_Reference/remove_meta_box
