Hi,
I think that you didn't understand my answer.
The address_template is used by email, order and invoices : When the address is display only with text.
Using custom fields ordering is the correct method for the address edition in the checkout (and other front-end/back-end forms).
You "pink" zone the address_template, the content that you posted on your first message.
The popup zone you the custom fields, your configuration send in your last message.
I don't see any problem.
The pink zone display the address_template content correctly (because it is only text) and the poup display custom fields with the right order.
Regards,