I see you have an additional card plugged in, a Soundblaster? This will require a PCI-e lane, and, the most logical place to steal it from might be your storage.
Perhaps experiment with removing the Soundblaster and retesting...(as a minimum, might be some bandwidth sharing limiting your speeds)
Does your mainboard have a pair of NVME slots?
Yeah so I thought that might be the problem, but I removed the card and tested the speeds again. The exact same thing, I have no idea what is going on here, this bios isn't very helpful either, couldn't find anything there.
And yeah it does have a second slot, and that's connected to the chipset, haven't tried it yet but why in the world would the first slot be limited to 2 lanes only or be getting x2 speeds when it's supposed to be Gen 3 x 4, even the wd dashboard confirms that? And it's not my 10900k, msi support tried to blame it on that but they don't know what they're talking about.
I know on some other z490 motherboards like asus, there is a lane allocation option, and you can change it from x2 to x4, but I have no such option