To make things less confusing unused features usually have a way to be turned off via grounding pins or permanently set firmware/BIOS options.

Often there are unused devices that are not used integrated into various chips and components in most electronics (not just computers). Intel is not going to make 8 versions of a CPU with different configurations. They just did not utilize it for cost or space considerations.

Its not that 'OEMs are indeed stupid and use USB 3.0 controllers, but use 2.0 ports.' Its more often that the engineers had a price point and a feature list they were given. If you look at the datasheet for the Intel Atom Z3735F processor in these both devices likely exist on the CPU chip itself, USB for sure and serial port more than likely. On my ASUS X205TA not only do I have a USB3.0 controller that shows up but in not broken out there is also a hardware com1 port. So there is often devices on these smaller netbooks not utilized. Which means they put everything including the kitchen sink onboard the CPU. Intel Atom processors are a SoC or system on a chip.

Via usb extensible host controller xbox