From end users point, it looks nothing different in functionality… But actually its different in terms of how you manage frappe/erpnext in long term.
Its highly recommend to always use Customize form to add custom fields… Its database site specific and you can update frappe and erpnext smoothly.
The reason is… editing doctype directly will affect its repo files e.g. Json files etc… And it can cause conflicts when you update frappe erpnext.
Unless you want to add custom doctype for custom cases … For this you have to maintain it under custom app to avoid hassles in long term maintenance