@ik1wvq - You have correctly identified that PA11 and PA12 are USBDM and USBDP.
However, the USB specification allows for different communication speeds. A USB 1.2 device signals the host which speed it is able to work at by pulling up either USBDM or USBDP with a resistor to 3.3V or (a little) higher.
The pull-up could be a fixed resistor, connected to 3.3V. Once pulled-up, the host asks the device for some details about itself ('enumeration'), and then acts accordingly.
However, Maple is more flexible than a single fixed USB device. Maple can change the type of USB device it implements dynamically. That requires the pull-up resistor to be activated under program control. That is what the DISC pin is doing. It can pull up the USBDP line, to signal its speed (12Mbits), and that it is ready to 'enumerate'.
So if the DISC pin is active, the USBDP signal will be pulled high. Hence you need to disable the DISC pin so that it doesn't pull USBDP high.
IIRC issuing a "USBSerial.end()" will disable the DISC signal, and the two USB pins can be used as GPIO (don;t connect them to a USB host, of course).
(Full disclosure: I am not a member of LeafLabs staff.)