Starting with version 1.7.0 the PDF Customizer module has the ability to attach one more additional file to an email. You need to install the 'amasty/module-pdf-custom-subscription-functionality' package from composer suggest to use this functionality (the functionality is available as a part of an active product subscription or support subscription).
When navigating to the PDF template (Marketing > Promotions > PDF Templates), you will find a new Upload an Additional File field:
The uploaded file is automatically added as an attachment to the email generated using the current template (along with the PDF document for the order/invoice/etc.). In other words, two files are attached to the email at the same time.