Is it correct that this is for custom hardware? I ask because Jetson does not expose other DP/DM pairs to the breakout headers (J3A1/J3A2).
Looking at section 19.4 it appears to me as if the actual ports used are separate from the controllers which can use those ports. In general, USB3 provides USB2 compatibility in the tegra124 via “companion” USB2 ports, rather than dedicated USB2 ports within that USB3 controller (the USB3 controller has dedicated USB3 handling, while USB2 on a USB3 port depends on outside ports to send data to the USB3 controller…this consumes a port which would otherwise be used on a USB2 controller).
Although I am uncertain of this, it looks like pinmux/padctl means total available ports at any one moment will not increase by using only USB2 on the USB3 controller…I believe pinmux means at least one USB2 port detaches or attaches to one and only one USB controller, regardless of that controller being USB2 or USB3, keeping total port count constant (only the controller used for that port changes). Perhaps someone with more detailed knowledge can verify that using USB3 controllers for only USB2 does not expose more ports.