This is May from Shopify.
Thank you for posting on our forums. I can understand how this will be beneficial to your business. I would be than happy to launch a feature request with our team to see if having separate invoices for subscription cost and shipping labels can be done in the future. While I can't guarantee that this feature will be added, I'm more than happy to pass along your suggestions that would provide better services to the Shopify platform.
Thank you again for bringing this up to us, and for your feedback. Feel free to reply back to this thread or contact our 24/7 support if you have further questions and concerns!