As Bob-The-Khun suggested, resetting the USB peripheral solves the huge startup delays that happen when a WDT reset happens and we are connected through the native port

Marlin/src/HAL/HAL_DUE/usb/usb_task.c

 
   uint16_t *ptr;
 
+  // Disable USB peripheral so we start clean and avoid lockups
+  otg_disable();
   udd_disable();
+
+  // Set the USB interrupt to our stack
   UDD_SetStack(&USBD_ISR);
 
   // Start USB stack to authorize VBus monitoring