Intel Atom processors are a SoC or system on a chip. Which means they put everything including the kitchen sink onboard the CPU. So there is often devices on these smaller netbooks not utilized.
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.
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. 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. They just did not utilize it for cost or space considerations.
Intel is not going to make 8 versions of a CPU with different configurations. Often there are unused devices that are not used integrated into various chips and components in most electronics (not just computers). To make things less confusing unused features usually have a way to be turned off via grounding pins or permanently set firmware/BIOS options. Sometimes manufactures don't do it, can't do it, or planned to have that feature and it gets hastily taken off to save space or cost at the last minute.
One common example of this is most newer i3/i5/i7 Intel processors support up to 4 monitors while many motherboards only have 1 monitor connector. It is becoming more common for motherboards with integrated graphics to have 2 and sometimes 3 monitor connectors but there still are not that many motherboards that break out all 4 display ports.
What you're seeing is common with newer hardware at all levels.