You said having the x399 prof.. so it has 3 ethernet port with the 10gb , the red one. So it's all on-board using the chipset Aquantia. In the nic list, do you have 3 port show ?  and 1 at 10gb ?

For the usb, you can pass the whole controller. Are you booting from an usb key ? Try to install into an ssd and then pass the whole ctrl to esxi. You will end up probably having 1 full usb ctrl to pass over 1 vm. Let me know, i will try to check with one of the my friend with another x399 board to see if...