You seem to live in a parallel universe... There has never ever been a 2.5Gbps USB 3.0 standard. I have met all of the USB 3.0 chip makers over the years and I was the first and I think only journalist that did a comparison of all the different USB 3.0 host controller available at the point when USB 3.0 was still new-ish. Unfortunately the publication I worked for back then has managed to lose all the pictures, so not much point in sharing it. I tested the the AMD A75 chipset, the ASMedia ASM1042, the Etron EJ168A, the Fresco Logic FL1009, the NEC/Renesas µD720200, the Renesas µD720201 and the VLI VL800 in 2011 and none of them had any other rating than 5Gbps. Back then it wasn't possible to reach the speeds of today, as the device controllers weren't fast enough. Fujitsu had a solution that could do 3.2Gbps/400MB/s. However, today it's not so hard with a nice fast SSD and a moder device controller.
I also don't think that you understand the technical aspects of how a motherboard chipset works, but let me see if I can help with that.
Below is a very rough layout of the available lanes/ports inside the Intel Skylake chipset (more recent chipsets from Intel adds USB 3.1 gen 2).
So as you can see, each of the USB ports that comes from a chipset are allocated one of 10 possible lanes. These lanes have the same width as a PCIe lane. So yes, the physical USB ports might connect directly to the chipset, but in the case of Intel, a USB 3.1 gen 2 port would only have one lane of PCIe 3.0 worth of bandwidth available to it, as it wouldn't make sense for Intel to make a custom interface for USB that's faster than PCIe 3.0. This means that if you have an Intel chipset, you'll never see the maximum performance from any chipset connected USB 3.1 gen 2 ports. I would hazard a guess and say that it's likely that AMD has the same limitation, but as they haven't provided any documentation, I can't say for certain. This means that only a couple of third part PCIe 3.0 x2 host controllers can offer near full USB 3.1 gen 2 performance.
More about Intel's 300-series chipsets and lane integration here -
https://videocardz.com/76275/intel-releases-full-specifications-of-z390-chipset
Oh, one last thing, the interconnect between the chipset and the CPU today is simply four PCIe 3.0 lanes with a fancy name, nothing more, nothing less. So saying this is a fast interface is simply not true any more. Btw, a Northbrdige hasn't been used in PC architecture for around 8-9 years now, so I think you need to catch up on your tech know how.