The motherboard lacks a USB-C connector, while the case provides one.
The motherboard lacks a USB-C connector, while the case provides one.
You're asking if the lack of a USB-C header on your motherboard matters because you're using a case without a built-in USB-C port. It's not crucial—just ensure the case supports the necessary ports for your needs.
I'm not very experienced with these things, but I think your setup could work. Your USB-C header should connect to the USB 3.0 port on your motherboard.